1
|
Wakamoto T, Yamamoto J, Senzaki S, Koide R, Kitazawa S, Kitahara R. Amplification of the Specific Conformational Fluctuation of Proteins by Site-Specific Mutagenesis and Hydrostatic Pressure. J Phys Chem B 2022; 126:1868-1875. [PMID: 35213155 DOI: 10.1021/acs.jpcb.1c10082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Conformational fluctuation, namely, protein interconversion between different conformations, is crucial to protein function. Outer surface protein A (OspA), comprising N- and C-terminal globular domains linked by a central β-sheet, is expressed on the surface of Borrelia burgdorferi, the causative agent of Lyme disease, and recognizes the TROSPA receptor in the tick gut. Solution nuclear magnetic resonance studies have shown that the central β-sheet and C-terminal domain containing TROSPA recognition sites are less stable than the N-terminal domain, revealing an intermediate conformation between the basic folded and completely unfolded proteins. We previously suggested that exposure of receptor-binding sites following denaturation of the C-terminal domain is advantageous for OspA binding to the receptor. Here, we observed amplification of a specific protein fluctuation by pressure perturbation and site-specific mutagenesis. The salt-bridge-destabilized mutant E160D and the cavity-enlarged mutant I243A favored the intermediate. The proportion of the intermediate accounted for almost 100% in E160D at 250 MPa. Strategies using a suitably chosen point mutation with high pressure are generally applicable for amplification of specific conformational fluctuation and potentially improve our understanding of the intermediate conformations of proteins. Knowledge of various conformations, including OspA intermediates, may be useful for designing a vaccine for Lyme disease.
Collapse
Affiliation(s)
- Takuro Wakamoto
- Graduate School of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan
| | - Junya Yamamoto
- Graduate School of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan
| | - Sho Senzaki
- College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan
| | - Reina Koide
- College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan
| | - Soichiro Kitazawa
- College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan
| | - Ryo Kitahara
- Graduate School of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan.,College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan
| |
Collapse
|
2
|
Wakamoto T, Kitazawa S, Kameda T, Kitahara R. Dynamic aspects of pressure and temperature-stabilized intermediates of outer surface protein A. Proteins 2020; 88:1423-1433. [PMID: 32519353 DOI: 10.1002/prot.25962] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/05/2020] [Accepted: 06/06/2020] [Indexed: 01/18/2023]
Abstract
Structural characterization of alternatively folded and partially disordered protein conformations remains challenging. Outer surface protein A (OspA) is a pivotal protein in Borrelia infection, which is the etiological agent of Lyme disease. OspA exists in equilibrium with intermediate conformations, in which the central and the C-terminal regions of the protein have lower stabilities than the N-terminal. Here, we characterize pressure- and temperature-stabilized intermediates of OspA by nuclear magnetic resonance spectroscopy combined with paramagnetic relaxation enhancement (PRE). We found that although the C-terminal region of the intermediate was partially disordered, it retains weak specific contact with the N-terminal region, owing to a twist of the central β-sheet and increased flexibility in the polypeptide chain. The disordered C-terminal region of the pressure-stabilized intermediate was more compact than that of the temperature-stabilized form. Further, molecular dynamics simulation demonstrated that temperature-induced disordering of the β-sheet was initiated at the C-terminal region and continued through to the central region. An ensemble of simulation snapshots qualitatively described the PRE data from the intermediate and indicated that the intermediate structures of OspA may expose tick receptor-binding sites more readily than does the basic folded conformation.
Collapse
Affiliation(s)
- Takuro Wakamoto
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Japan
| | - Soichiro Kitazawa
- College of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, Japan
| | - Tomoshi Kameda
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Ryo Kitahara
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Japan.,College of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, Japan
| |
Collapse
|
3
|
Makabe K, Nakamura T, Dhar D, Ikura T, Koide S, Kuwajima K. An Overlapping Region between the Two Terminal Folding Units of the Outer Surface Protein A (OspA) Controls Its Folding Behavior. J Mol Biol 2018; 430:1799-1813. [PMID: 29709572 DOI: 10.1016/j.jmb.2018.04.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 04/12/2018] [Accepted: 04/18/2018] [Indexed: 10/17/2022]
Abstract
Although many naturally occurring proteins consist of multiple domains, most studies on protein folding to date deal with single-domain proteins or isolated domains of multi-domain proteins. Studies of multi-domain protein folding are required for further advancing our understanding of protein folding mechanisms. Borrelia outer surface protein A (OspA) is a β-rich two-domain protein, in which two globular domains are connected by a rigid and stable single-layer β-sheet. Thus, OspA is particularly suited as a model system for studying the interplays of domains in protein folding. Here, we studied the equilibria and kinetics of the urea-induced folding-unfolding reactions of OspA probed with tryptophan fluorescence and ultraviolet circular dichroism. Global analysis of the experimental data revealed compelling lines of evidence for accumulation of an on-pathway intermediate during kinetic refolding and for the identity between the kinetic intermediate and a previously described equilibrium unfolding intermediate. The results suggest that the intermediate has the fully native structure in the N-terminal domain and the single layer β-sheet, with the C-terminal domain still unfolded. The observation of the productive on-pathway folding intermediate clearly indicates substantial interactions between the two domains mediated by the single-layer β-sheet. We propose that a rigid and stable intervening region between two domains creates an overlap between two folding units and can energetically couple their folding reactions.
Collapse
Affiliation(s)
- Koki Makabe
- Graduate School of Science and Engineering, Yamagata University, Jyonan 4-3-16, Yonezawa, Yamagata 992-8510, Japan; Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan; Department of Functional Molecular Science, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan.
| | - Takashi Nakamura
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
| | - Debanjan Dhar
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
| | - Teikichi Ikura
- Laboratory of Structural Biology, School of Biomedical Science, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Shohei Koide
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, and Perlmutter Cancer Center at NYU Langone Health, New York, NY 10016, USA
| | - Kunihiro Kuwajima
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan; Department of Functional Molecular Science, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan; Department of Physics, School of Science, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; School of Computational Sciences, Korea Institute for Advanced Study (KIAS), Dongdaemun-gu, Seoul 130-722, Korea
| |
Collapse
|
4
|
Kitahara R, Simorellis A, Hata K, Maeno A, Yokoyama S, Koide S, Akasaka K. A delicate interplay of structure, dynamics, and thermodynamics for function: a high pressure NMR study of outer surface protein A. Biophys J 2012; 102:916-26. [PMID: 22385863 PMCID: PMC3283806 DOI: 10.1016/j.bpj.2011.12.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 11/23/2011] [Accepted: 12/01/2011] [Indexed: 10/28/2022] Open
Abstract
Outer surface protein A (OspA) is a crucial protein in the infection of Borrelia burgdorferi causing Lyme disease. We studied conformational fluctuations of OspA with high-pressure (15)N/(1)H two-dimensional NMR along with high-pressure fluorescence spectroscopy. We found evidence within folded, native OspA for rapid local fluctuations of the polypeptide backbone in the nonglobular single layer β-sheet connecting the N- and C-terminal domains with τ << ms, which may give the two domains certain independence in mobility and thermodynamic stability. Furthermore, we found that folded, native OspA is in equilibrium (τ >> ms) with a minor conformer I, which is almost fully disordered and hydrated for the entire C-terminal part of the polypeptide chain from β8 to the C-terminus. Conformer I is characterized with ΔG(0) = 32 ± 9 kJ/mol and ΔV(0) = -140 ± 40 mL/mol, populating only ∼0.001% at 40°C at 0.1 MPa, pH 5.9. Because in the folded conformer the receptor binding epitope of OspA is buried in the C-terminal domain, its transition into conformer I under in vivo conditions may be critical for the infection of B. burgdorferi. The formation and stability of the peculiar conformer I are apparently supported by a large packing defect or cavity located in the C-terminal domain.
Collapse
Affiliation(s)
- Ryo Kitahara
- College of Pharmaceutical Sciences, Ritsumeikan University, Shiga, Japan
- RIKEN SPring-8 Center, Hyogo, Japan
| | | | - Kazumi Hata
- College of Pharmaceutical Sciences, Ritsumeikan University, Shiga, Japan
- RIKEN SPring-8 Center, Hyogo, Japan
| | - Akihiro Maeno
- RIKEN SPring-8 Center, Hyogo, Japan
- High Pressure Protein Research Center, Institute of Advanced Technology, Kinki University, Wakayama, Japan
| | - Shigeyuki Yokoyama
- RIKEN Systems and Structural Biology Center, Yokohama, Japan
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Shohei Koide
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois
| | - Kazuyuki Akasaka
- RIKEN SPring-8 Center, Hyogo, Japan
- High Pressure Protein Research Center, Institute of Advanced Technology, Kinki University, Wakayama, Japan
| |
Collapse
|
5
|
Schulze RJ, Chen S, Kumru OS, Zückert WR. Translocation of Borrelia burgdorferi surface lipoprotein OspA through the outer membrane requires an unfolded conformation and can initiate at the C-terminus. Mol Microbiol 2010; 76:1266-78. [PMID: 20398211 DOI: 10.1111/j.1365-2958.2010.07172.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Borrelia burgdorferi surface lipoproteins are essential to the pathogenesis of Lyme borreliosis, but the mechanisms responsible for their localization are only beginning to emerge. We have previously demonstrated the critical nature of the amino-terminal 'tether' domain of the mature lipoprotein for sorting a fluorescent reporter to the Borrelia cell surface. Here, we show that individual deletion of four contiguous residues within the tether of major surface lipoprotein OspA results in its inefficient translocation across the Borrelia outer membrane. Intriguingly, C-terminal epitope tags of these N-terminal deletion mutants were selectively surface-exposed. Fold-destabilizing C-terminal point mutations and deletions did not block OspA secretion, but rather restored one of the otherwise periplasmic tether mutants to the bacterial surface. Together, these data indicate that disturbance of a confined tether feature leads to premature folding of OspA in the periplasm and thereby prevents secretion through the outer membrane. Furthermore, they suggest that OspA emerges tail-first on the bacterial surface, yet independent of a specific C-terminal targeting peptide sequence.
Collapse
Affiliation(s)
- Ryan J Schulze
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Mail Stop 3029, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA
| | | | | | | |
Collapse
|
6
|
Tarafdar PK, Vedantam LV, Kondreddy A, Podile AR, Swamy MJ. Biophysical investigations on the aggregation and thermal unfolding of harpinPss and identification of leucine-zipper-like motifs in harpins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:1684-92. [DOI: 10.1016/j.bbapap.2009.07.023] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2009] [Revised: 07/11/2009] [Accepted: 07/31/2009] [Indexed: 11/17/2022]
|
7
|
Lee BM, Buck-Koehntop BA, Martinez-Yamout MA, Dyson HJ, Wright PE. Embryonic neural inducing factor churchill is not a DNA-binding zinc finger protein: solution structure reveals a solvent-exposed beta-sheet and zinc binuclear cluster. J Mol Biol 2007; 371:1274-89. [PMID: 17610897 PMCID: PMC1994575 DOI: 10.1016/j.jmb.2007.06.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2007] [Revised: 06/06/2007] [Accepted: 06/07/2007] [Indexed: 11/20/2022]
Abstract
Churchill is a zinc-containing protein that is involved in neural induction during embryogenesis. At the time of its discovery, it was thought on the basis of sequence alignment to contain two zinc fingers of the C4 type. Further, binding of an N-terminal GST-Churchill fusion protein to a particular DNA sequence was demonstrated by immunoprecipitation selection assay, suggesting that Churchill may function as a transcriptional regulator by sequence-specific DNA binding. We show by NMR solution structure determination that, far from containing canonical C4 zinc fingers, the protein contains three bound zinc ions in novel coordination sites, including an unusual binuclear zinc cluster. The secondary structure of Churchill is also unusual, consisting of a highly solvent-exposed single-layer beta-sheet. Hydrogen-deuterium exchange and backbone relaxation measurements reveal that Churchill is unusually dynamic on a number of time scales, with the exception of regions surrounding the zinc coordinating sites, which serve to stabilize the otherwise unstructured N terminus and the single-layer beta-sheet. No binding of Churchill to the previously identified DNA sequence could be detected, and extensive searches using DNA sequence selection techniques could find no other DNA sequence that was bound by Churchill. Since the N-terminal amino acids of Churchill form part of the zinc-binding motif, the addition of a fusion protein at the N terminus causes loss of zinc and unfolding of Churchill. This observation most likely explains the published DNA-binding results, which would arise due to non-specific interaction of the unfolded protein in the immunoprecipitation selection assay. Since Churchill does not appear to bind DNA, we suggest that it may function in embryogenesis as a protein-interaction factor.
Collapse
Affiliation(s)
- Brian M Lee
- Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | | | | | | | | |
Collapse
|
8
|
Safarian S, Alimohammadi M, Saberi AA, Moosavi-Movahedi AA. A statistical mechanical deconvolution of the differential scanning calorimetric profiles of the thermal denaturation of cyanomethemoglobin. Protein J 2005; 24:175-81. [PMID: 16096723 DOI: 10.1007/s10930-005-7841-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
A differential scanning calorimetric study of the thermal unfolding of horse cyanomethemoglobin (as an irreversible protein system) was carried out in phosphate-EDTA buffer (20 mM phosphate, 1 mM EDTA) pH 7.2. The calorimetric rescanning of the protein solution was found to be irreversible and the process unfolded state --> final state appears to follow first order kinetic. Assuming the system to be comprised of n reversible states and one irreversible final state, the number of particles participating in the reversible states changes with time because they ultimately transit to the final irreversible denatured state. Hence, we carried out the deconvolution analysis using the grand canonical ensembles instead of just the canonical ensembles. This change was effected by introducing a correction term into the related equations which determines the outlet share of those particles exiting from the reversible states and converting into the final irreversible state. This approach provided an improved interpretation of the experimental data, which supports the following two-step process for the thermal denaturation of cyanomethemoglobin: alpha(2)beta(2) --> (alpha + alphabeta + beta)(excited) --> alpha(melt) + (alphabeta)(melt) + (beta(melt).
Collapse
Affiliation(s)
- Shahrokh Safarian
- Department of Biology, Faculty of Science, University of Tehran, Tehran, Iran.
| | | | | | | |
Collapse
|
9
|
Koide S, Yang X, Huang X, Dunn JJ, Luft BJ. Structure-based Design of a Second-generation Lyme Disease Vaccine Based on a C-terminal Fragment of Borrelia burgdorferi OspA. J Mol Biol 2005; 350:290-9. [PMID: 15935380 DOI: 10.1016/j.jmb.2005.04.066] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2004] [Revised: 04/25/2005] [Accepted: 04/27/2005] [Indexed: 11/30/2022]
Abstract
Here, we describe a structure-based approach to reduce the size of an antigen protein for a subunit vaccine. Our method consists of (i) determining the three-dimensional structure of an antigen, (ii) identifying protective epitopes, (iii) generation of an antigen fragment that contains the protective epitope, and (iv) rational design to compensate for destabilization caused by truncation. Using this approach we have successfully developed a second-generation Lyme disease vaccine. Outer surface protein A (OspA) from the Lyme disease spirochete Borrelia burgdorferi elicits protective immunity that blocks transmission of Borrelia from the tick vector to the vaccinated animal, and thus has been a focus of vaccine development. OspA has two globular domains that are connected via a unique single-layer beta-sheet. All anti-OspA monoclonal antibodies that block Borrelia transmission bind to conformational epitopes in the C-terminal domain of OspA, suggesting the possibility of using the C-terminal domain alone as a recombinant protein-based vaccine. The removal of ineffective parts from the OspA antigen may reduce side effects and lead to a safer vaccine. We prepared a C-terminal fragment of OspA by removing approximately 45% of residues from the N terminus. Although the fragment retained the native conformation and affinity to a protective antibody, its vaccine efficacy and conformational stability were significantly reduced with respect to full-length OspA. We successfully stabilized the fragment by replacing amino acid residues involved in buried salt-bridges with residues promoting hydrophobic interactions. The mutations promoted the vaccine efficacy of the redesigned fragment to a level comparable to that of the full-length protein, demonstrating the importance of the antigen stability for OspA's vaccine efficacy. Our strategy should be useful for further refining OspA-based vaccines and developing recombinant vaccines for other diseases.
Collapse
MESH Headings
- Animals
- Antibodies, Bacterial/immunology
- Antibodies, Monoclonal/immunology
- Antibody Affinity
- Antigens, Bacterial/chemistry
- Antigens, Bacterial/immunology
- Antigens, Surface/chemistry
- Antigens, Surface/immunology
- Bacterial Outer Membrane Proteins/chemistry
- Bacterial Outer Membrane Proteins/immunology
- Bacterial Vaccines
- Borrelia burgdorferi/chemistry
- Borrelia burgdorferi/immunology
- Enzyme-Linked Immunosorbent Assay
- Epitope Mapping
- Female
- Hydrophobic and Hydrophilic Interactions
- Lipoproteins/chemistry
- Lipoproteins/immunology
- Lyme Disease Vaccines/chemistry
- Lyme Disease Vaccines/immunology
- Magnetic Resonance Spectroscopy
- Mice
- Mice, Inbred C3H
- Models, Molecular
- Peptide Fragments/chemistry
- Peptide Fragments/immunology
- Protein Conformation
- Static Electricity
- Structure-Activity Relationship
- Vaccination
- Vaccines, Subunit/chemistry
- Vaccines, Subunit/immunology
Collapse
Affiliation(s)
- Shohei Koide
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA.
| | | | | | | | | |
Collapse
|
10
|
Yan S, Gawlak G, Smith J, Silver L, Koide A, Koide S. Conformational Heterogeneity of an Equilibrium Folding Intermediate Quantified and Mapped by Scanning Mutagenesis. J Mol Biol 2004; 338:811-25. [PMID: 15099747 DOI: 10.1016/j.jmb.2004.02.063] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2003] [Revised: 02/23/2004] [Accepted: 02/24/2004] [Indexed: 11/18/2022]
Abstract
It is challenging to experimentally define an energy landscape for protein folding that comprises multiple partially unfolded states. Experimental results are often ambiguous as to whether a non-native state is conformationally homogeneous. Here, we tested an approach combining systematic mutagenesis and a Brønsted-like analysis to reveal and quantify conformational heterogeneity of folding intermediate states. Using this method, we resolved an otherwise apparently homogeneous equilibrium folding intermediate of Borrelia burgdorferi OspA into two conformationally distinct species and determined their relative populations. Furthermore, we mapped the structural differences between these intermediate species, which are consistent with the non-native species that we previously proposed based on native-state hydrogen exchange studies. When treated as a single state, the intermediate ensemble exhibited fractional Phi-values for mutations and Hammond-type behaviors that are often observed for folding transition states. We found that a change in relative population of the two species within the intermediate ensemble explains these properties well, suggesting that fractional Phi-values and Hammond-type behaviors exhibited by folding intermediates and transition states may arise more often from conformational heterogeneity than from a single partial structure. Our results are consistent with the presence of multiple minima in a rugged energy landscape predicted from theoretical studies. The method described here provides a promising means to probe a complex folding energy landscape.
Collapse
Affiliation(s)
- Shude Yan
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | | | | | | | | | | |
Collapse
|