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Okuda-Shimazaki J, Yoshida H, Lee I, Kojima K, Suzuki N, Tsugawa W, Yamada M, Inaka K, Tanaka H, Sode K. Microgravity environment grown crystal structure information based engineering of direct electron transfer type glucose dehydrogenase. Commun Biol 2022; 5:1334. [PMID: 36473944 PMCID: PMC9727119 DOI: 10.1038/s42003-022-04286-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022] Open
Abstract
The heterotrimeric flavin adenine dinucleotide dependent glucose dehydrogenase is a promising enzyme for direct electron transfer (DET) principle-based glucose sensors within continuous glucose monitoring systems. We elucidate the structure of the subunit interface of this enzyme by preparing heterotrimer complex protein crystals grown under a space microgravity environment. Based on the proposed structure, we introduce inter-subunit disulfide bonds between the small and electron transfer subunits (5 pairs), as well as the catalytic and the electron transfer subunits (9 pairs). Without compromising the enzyme's catalytic efficiency, a mutant enzyme harboring Pro205Cys in the catalytic subunit, Asp383Cys and Tyr349Cys in the electron transfer subunit, and Lys155Cys in the small subunit, is determined to be the most stable of the variants. The developed engineered enzyme demonstrate a higher catalytic activity and DET ability than the wild type. This mutant retains its full activity below 70 °C as well as after incubation at 75 °C for 15 min - much higher temperatures than the current gold standard enzyme, glucose oxidase, is capable of withstanding.
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Affiliation(s)
- Junko Okuda-Shimazaki
- grid.10698.360000000122483208Joint Department of Biomedical Engineering, The University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC27599 USA
| | - Hiromi Yoshida
- grid.258331.e0000 0000 8662 309XDepartment of Basic Life Science, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793 Japan
| | - Inyoung Lee
- grid.10698.360000000122483208Joint Department of Biomedical Engineering, The University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC27599 USA
| | - Katsuhiro Kojima
- grid.136594.c0000 0001 0689 5974Graduate School of Engineering, Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588 Japan
| | - Nanoha Suzuki
- grid.136594.c0000 0001 0689 5974Graduate School of Engineering, Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588 Japan
| | - Wakako Tsugawa
- grid.136594.c0000 0001 0689 5974Graduate School of Engineering, Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588 Japan
| | - Mitsugu Yamada
- grid.62167.340000 0001 2220 7916JEM Utilization Center Human Spaceflight Technology Directorate, Japan Aerospace Exploration Agency (JAXA), 2-1-1 Sengen, Tsukuba-shi, Ibaraki 305-8505 Japan
| | - Koji Inaka
- grid.459744.fMaruwa Foods and Biosciences, 170-1 Tsutsui-cho, Yamato Koriyama-shi, Nara 639-1123 Japan
| | - Hiroaki Tanaka
- grid.459486.2Confocal Science Inc., Musashino Bldg, 5-14-15 Fukasawa, Setagaya-ku, Tokyo 158-0081 Japan
| | - Koji Sode
- grid.10698.360000000122483208Joint Department of Biomedical Engineering, The University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC27599 USA
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2
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Deplazes E, Chin YKY, King GF, Mancera RL. The unusual conformation of cross-strand disulfide bonds is critical to the stability of β-hairpin peptides. Proteins 2019; 88:485-502. [PMID: 31589791 DOI: 10.1002/prot.25828] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 08/27/2019] [Accepted: 09/17/2019] [Indexed: 01/04/2023]
Abstract
The cross-strand disulfides (CSDs) found in β-hairpin antimicrobial peptides (β-AMPs) show a unique disulfide geometry that is characterized by unusual torsion angles and a short Cα-Cα distance. While the sequence and disulfide bond connectivity of disulfide-rich peptides is well studied, much less is known about the disulfide geometry found in CSDs and their role in the stability of β-AMPs. To address this, we solved the nuclear magnetic resonance (NMR) structure of the β-AMP gomesin (Gm) at 278, 298, and 310 K, examined the disulfide bond geometry of over 800 disulfide-rich peptides, and carried out extensive molecular dynamics (MD) simulation of the peptides Gm and protegrin. The NMR data suggests Cα-Cα distances characteristic for CSDs are independent of temperature. Analysis of disulfide-rich peptides from the Protein Data Bank revealed that right-handed and left-handed rotamers are equally likely in CSDs. The previously reported preference for right-handed rotamers was likely biased by restricting the analysis to peptides and proteins solved using X-ray crystallography. Furthermore, data from MD simulations showed that the short Cα-Cα distance is critical for the stability of these peptides. The unique disulfide geometry of CSDs poses a challenge to biomolecular force fields and to retain the stability of β-hairpin fold over long simulation times, restraints on the torsion angles might be required.
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Affiliation(s)
- Evelyne Deplazes
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and Curtin Institute for Computation, Curtin University, Perth, Western Australia, Australia
| | - Yanni K-Y Chin
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia
| | - Glenn F King
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia
| | - Ricardo L Mancera
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and Curtin Institute for Computation, Curtin University, Perth, Western Australia, Australia
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3
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Haworth NL, Wouters MJ, Hunter MO, Ma L, Wouters MA. Cross-strand disulfides in the hydrogen bonding site of antiparallel β-sheet (aCSDhs): Forbidden disulfides that are highly strained, easily broken. Protein Sci 2018; 28:239-256. [PMID: 30383331 DOI: 10.1002/pro.3545] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 10/30/2018] [Accepted: 10/30/2018] [Indexed: 12/16/2022]
Abstract
Some disulfide bonds perform important structural roles in proteins, but another group has functional roles via redox reactions. Forbidden disulfides are stressed disulfides found in recognizable protein contexts, which currently constitute more than 10% of all disulfides in the PDB. They likely have functional redox roles and constitute a major subset of all redox-active disulfides. The torsional strain of forbidden disulfides is typically higher than for structural disulfides, but not so high as to render them immediately susceptible to reduction under physionormal conditions. Previously we characterized the most abundant forbidden disulfide in the Protein Data Bank, the aCSDn: a canonical motif in which disulfide-bonded cysteine residues are positioned directly opposite each other on adjacent anti-parallel β-strands such that the backbone hydrogen-bonded moieties are directed away from each other. Here we perform a similar analysis for the aCSDh, a less common motif in which the opposed cysteine residues are backbone hydrogen bonded. Oxidation of two Cys in this context places significant strain on the protein system, with the β-chains tilting toward each other to allow disulfide formation. Only left-handed aCSDh conformations are compatible with the inherent right-handed twist of β-sheets. aCSDhs tend to be more highly strained than aCSDns, particularly when both hydrogen bonds are formed. We discuss characterized roles of aCSDh motifs in proteins of the dataset, which include catalytic disulfides in ribonucleotide reductase and ahpC peroxidase as well as a redox-active disulfide in P1 lysozyme, involved in a major conformation change. The dataset also includes many binding proteins.
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Affiliation(s)
- Naomi L Haworth
- Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia.,Structural & Computational Biology Division, Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia
| | - Michael J Wouters
- Electricity Section, National Measurement Institute, Lindfield, New South Wales, Australia
| | - Morgan O Hunter
- Bioinformatics, Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia.,School of Cancer Medicine, La Trobe University, Melbourne, Victoria, Australia
| | - Lixia Ma
- School of Statistics, Henan University of Economics and Law, Henan Province, China
| | - Merridee A Wouters
- Bioinformatics, Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia.,School of Cancer Medicine, La Trobe University, Melbourne, Victoria, Australia.,Cancer Data Science, Children's Medical Research Institute, Westmead, New South Wales, Australia
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4
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Santhanagopalan I, Degiacomi MT, Shepherd DA, Hochberg GKA, Benesch JLP, Vierling E. It takes a dimer to tango: Oligomeric small heat shock proteins dissociate to capture substrate. J Biol Chem 2018; 293:19511-19521. [PMID: 30348902 DOI: 10.1074/jbc.ra118.005421] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 10/12/2018] [Indexed: 12/23/2022] Open
Abstract
Small heat-shock proteins (sHsps) are ubiquitous molecular chaperones, and sHsp mutations or altered expression are linked to multiple human disease states. sHsp monomers assemble into large oligomers with dimeric substructure, and the dynamics of sHsp oligomers has led to major questions about the form that captures substrate, a critical aspect of their mechanism of action. We show here that substructural dimers of two plant dodecameric sHsps, Ta16.9 and homologous Ps18.1, are functional units in the initial encounter with unfolding substrate. We introduced inter-polypeptide disulfide bonds at the two dodecameric interfaces, dimeric and nondimeric, to restrict how their assemblies can dissociate. When disulfide-bonded at the nondimeric interface, mutants of Ta16.9 and Ps18.1 (TaCT-ACD and PsCT-ACD) were inactive but, when reduced, had WT-like chaperone activity, demonstrating that dissociation at nondimeric interfaces is essential for sHsp activity. Moreover, the size of the TaCT-ACD and PsCT-ACD covalent unit defined a new tetrahedral geometry for these sHsps, different from that observed in the Ta16.9 X-ray structure. Importantly, oxidized Tadimer (disulfide bonded at the dimeric interface) exhibited greatly enhanced ability to protect substrate, indicating that strengthening the dimeric interface increases chaperone efficiency. Temperature-induced size and secondary structure changes revealed that folded sHsp dimers interact with substrate and that dimer stability affects chaperone efficiency. These results yield a model in which sHsp dimers capture substrate before assembly into larger, heterogeneous sHsp-substrate complexes for substrate refolding or degradation, and suggest that tuning the strength of the dimer interface can be used to engineer sHsp chaperone efficiency.
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Affiliation(s)
- Indu Santhanagopalan
- From the Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts 01003
| | - Matteo T Degiacomi
- Department of Chemistry, Physical & Theoretical Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, United Kingdom, and.,Department of Chemistry, Durham University, South Road, Durham, DH1 3LE, United Kingdom
| | - Dale A Shepherd
- Department of Chemistry, Physical & Theoretical Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, United Kingdom, and
| | - Georg K A Hochberg
- Department of Chemistry, Physical & Theoretical Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, United Kingdom, and
| | - Justin L P Benesch
- Department of Chemistry, Physical & Theoretical Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, United Kingdom, and
| | - Elizabeth Vierling
- From the Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts 01003,
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5
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Design, display and immunogenicity of HIV1 gp120 fragment immunogens on virus-like particles. Vaccine 2018; 36:6345-6353. [PMID: 30220462 DOI: 10.1016/j.vaccine.2018.07.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 06/26/2018] [Accepted: 07/16/2018] [Indexed: 12/17/2022]
Abstract
The broadly neutralizing antibody against HIV-1, b12, binds to the CD4 binding site (CD4bs) on the outer domain (OD) of the gp120 subunit of HIV-1 Env. We have previously reported the design of an E. coli expressed fragment of HIV-1 gp120, b122a, containing about 70% of the b12 epitope with the idea of focusing the immune response to this structure. Since the b122a structure was found to be only partially folded, as assessed by circular dichroism and protease resistance, we attempted to stabilize it by the introduction of additional disulfide bonds. One such mutant, b122a1-b showed increased stability and bound b12 with 30-fold greater affinity as compared to b122a. Various b122a and OD fragment proteins were displayed on the surface of Qβ virus-like particles. Sera raised against these particles in six-month long rabbit immunization studies could neutralize Tier1 viruses across different subtypes with the best results observed with b122a1-b displayed particles. Significantly higher amounts of antibodies directed towards the CD4bs were also elicited by particles displaying b122a1-b. This study highlights the ability of fragment immunogens to focus the antibody response to the conserved CD4bs of HIV-1.
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6
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Rathore U, Purwar M, Vignesh VS, Das R, Kumar AA, Bhattacharyya S, Arendt H, DeStefano J, Wilson A, Parks C, La Branche CC, Montefiori DC, Varadarajan R. Bacterially expressed HIV-1 gp120 outer-domain fragment immunogens with improved stability and affinity for CD4-binding site neutralizing antibodies. J Biol Chem 2018; 293:15002-15020. [PMID: 30093409 DOI: 10.1074/jbc.ra118.005006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Indexed: 12/20/2022] Open
Abstract
Protein minimization is an attractive approach for designing vaccines against rapidly evolving pathogens such as human immunodeficiency virus, type 1 (HIV-1), because it can help in focusing the immune response toward conserved conformational epitopes present on complex targets. The outer domain (OD) of HIV-1 gp120 contains epitopes for a large number of neutralizing antibodies and therefore is a primary target for structure-based vaccine design. We have previously designed a bacterially expressed outer-domain immunogen (ODEC) that bound CD4-binding site (CD4bs) ligands with 3-12 μm affinity and elicited a modest neutralizing antibody response in rabbits. In this study, we have optimized ODEC using consensus sequence design, cyclic permutation, and structure-guided mutations to generate a number of variants with improved yields, biophysical properties, stabilities, and affinities (KD of 10-50 nm) for various CD4bs targeting broadly neutralizing antibodies, including the germline-reverted version of the broadly neutralizing antibody VRC01. In contrast to ODEC, the optimized immunogens elicited high anti-gp120 titers in rabbits as early as 6 weeks post-immunization, before any gp120 boost was given. Following two gp120 boosts, sera collected at week 22 showed cross-clade neutralization of tier 1 HIV-1 viruses. Using a number of different prime/boost combinations, we have identified a cyclically permuted OD fragment as the best priming immunogen, and a trimeric, cyclically permuted gp120 as the most suitable boosting molecule among the tested immunogens. This study also provides insights into some of the biophysical correlates of improved immunogenicity.
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Affiliation(s)
- Ujjwal Rathore
- From the Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India 560012
| | - Mansi Purwar
- From the Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India 560012
| | | | - Raksha Das
- From the Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India 560012
| | - Aditya Arun Kumar
- From the Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India 560012
| | - Sanchari Bhattacharyya
- From the Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India 560012
| | - Heather Arendt
- the International AIDS Vaccine Initiative, Brooklyn, New York 11226, and
| | - Joanne DeStefano
- the International AIDS Vaccine Initiative, Brooklyn, New York 11226, and
| | - Aaron Wilson
- the International AIDS Vaccine Initiative, Brooklyn, New York 11226, and
| | - Christopher Parks
- the International AIDS Vaccine Initiative, Brooklyn, New York 11226, and
| | - Celia C La Branche
- the Department of Surgery, Duke University Medical Center, Durham, North Carolina 27707
| | - David C Montefiori
- the Department of Surgery, Duke University Medical Center, Durham, North Carolina 27707
| | - Raghavan Varadarajan
- From the Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India 560012,
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7
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Seid CA, Jones KM, Pollet J, Keegan B, Hudspeth E, Hammond M, Wei J, McAtee CP, Versteeg L, Gutierrez A, Liu Z, Zhan B, Respress JL, Strych U, Bottazzi ME, Hotez PJ. Cysteine mutagenesis improves the production without abrogating antigenicity of a recombinant protein vaccine candidate for human chagas disease. Hum Vaccin Immunother 2016; 13:621-633. [PMID: 27737611 DOI: 10.1080/21645515.2016.1242540] [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] [Indexed: 10/20/2022] Open
Abstract
A therapeutic vaccine for human Chagas disease is under development by the Sabin Vaccine Institute Product Development Partnership. The aim of the vaccine is to significantly reduce the parasite burden of Trypanosoma cruzi in humans, either as a standalone product or in combination with conventional chemotherapy. Vaccination of mice with Tc24 formulated with monophosphoryl-lipid A (MPLA) adjuvant results in a Th1 skewed immune response with elevated IgG2a and IFNγ levels and a statistically significant decrease in parasitemia following T. cruzi challenge. Tc24 was therefore selected for scale-up and further evaluation. During scale up and downstream process development, significant protein aggregation was observed due to intermolecular disulfide bond formation. To prevent protein aggregation, cysteine codons were replaced with serine codons which resulted in the production of a non-aggregated and soluble recombinant protein, Tc24-C4. No changes to the secondary structure of the modified molecule were detected by circular dichroism. Immunization of mice with wild-type Tc24 or Tc24-C4, formulated with E6020 (TLR4 agonist analog to MPLA) emulsified in a squalene-oil-in-water emulsion, resulted in IgG2a and antigen specific IFNγ production levels from splenocytes that were not significantly different, indicating that eliminating putative intermolecular disulfide bonds had no significant impact on the immunogenicity of the molecule. In addition, vaccination with either formulated wild type Tc24 or Tc24-C4 antigen also significantly increased survival and reduced cardiac parasite burden in mice. Investigations are now underway to examine the efficacy of Tc24-C4 formulated with other adjuvants to reduce parasite burden and increase survival in pre-clinical studies.
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Affiliation(s)
- Christopher A Seid
- a Sabin Vaccine Institute and Texas Children's Hospital Center for Vaccine Development , Houston , TX , USA
| | - Kathryn M Jones
- a Sabin Vaccine Institute and Texas Children's Hospital Center for Vaccine Development , Houston , TX , USA.,b Departments of Pediatrics and Molecular Virology and Microbiology , National School of Tropical Medicine, Baylor College of Medicine , Houston , TX , USA
| | - Jeroen Pollet
- a Sabin Vaccine Institute and Texas Children's Hospital Center for Vaccine Development , Houston , TX , USA.,b Departments of Pediatrics and Molecular Virology and Microbiology , National School of Tropical Medicine, Baylor College of Medicine , Houston , TX , USA
| | - Brian Keegan
- a Sabin Vaccine Institute and Texas Children's Hospital Center for Vaccine Development , Houston , TX , USA
| | - Elissa Hudspeth
- a Sabin Vaccine Institute and Texas Children's Hospital Center for Vaccine Development , Houston , TX , USA
| | - Molly Hammond
- a Sabin Vaccine Institute and Texas Children's Hospital Center for Vaccine Development , Houston , TX , USA
| | - Junfei Wei
- a Sabin Vaccine Institute and Texas Children's Hospital Center for Vaccine Development , Houston , TX , USA
| | - C Patrick McAtee
- a Sabin Vaccine Institute and Texas Children's Hospital Center for Vaccine Development , Houston , TX , USA
| | - Leroy Versteeg
- a Sabin Vaccine Institute and Texas Children's Hospital Center for Vaccine Development , Houston , TX , USA
| | - Amanda Gutierrez
- a Sabin Vaccine Institute and Texas Children's Hospital Center for Vaccine Development , Houston , TX , USA
| | - Zhuyun Liu
- a Sabin Vaccine Institute and Texas Children's Hospital Center for Vaccine Development , Houston , TX , USA
| | - Bin Zhan
- a Sabin Vaccine Institute and Texas Children's Hospital Center for Vaccine Development , Houston , TX , USA.,b Departments of Pediatrics and Molecular Virology and Microbiology , National School of Tropical Medicine, Baylor College of Medicine , Houston , TX , USA
| | - Jonathan L Respress
- d Southwest Electronic Energy Medical Research Institute (SWEMRI) , Missouri City , TX , USA
| | - Ulrich Strych
- a Sabin Vaccine Institute and Texas Children's Hospital Center for Vaccine Development , Houston , TX , USA.,b Departments of Pediatrics and Molecular Virology and Microbiology , National School of Tropical Medicine, Baylor College of Medicine , Houston , TX , USA
| | - Maria Elena Bottazzi
- a Sabin Vaccine Institute and Texas Children's Hospital Center for Vaccine Development , Houston , TX , USA.,b Departments of Pediatrics and Molecular Virology and Microbiology , National School of Tropical Medicine, Baylor College of Medicine , Houston , TX , USA
| | - Peter J Hotez
- a Sabin Vaccine Institute and Texas Children's Hospital Center for Vaccine Development , Houston , TX , USA.,b Departments of Pediatrics and Molecular Virology and Microbiology , National School of Tropical Medicine, Baylor College of Medicine , Houston , TX , USA.,c James A. Baker III Institute for Public Policy , Rice University , Houston , TX , USA
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8
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Cunha KC, Rusu VH, Viana IFT, Marques ETA, Dhalia R, Lins RD. Assessing protein conformational sampling and structural stability via de novo design and molecular dynamics simulations. Biopolymers 2016; 103:351-61. [PMID: 25677872 DOI: 10.1002/bip.22626] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 01/31/2015] [Accepted: 02/03/2015] [Indexed: 11/10/2022]
Abstract
Molecular dynamics and de novo techniques, associated to quality parameter sets, have excelled at determining the structure of small proteins with high accuracy. To achieve a detailed description of protein conformations, these methods must critically assess the thermodynamic features of the molecular ensembles. Here, a comparison of the conformational ensemble generated by molecular dynamics and de novo techniques were carried out for six Top7-based proteins carrying gp41 HIV-1 epitopes. The native Top7, a highly stable computationally designed protein, was used as benchmark. Structural stability, flexibility, and secondary structure content were assessed. The consistency of the latter was compared to experimental circular dichroism spectra for all proteins. While both methods are capable to identify the stable from unstable chimeric proteins, the sampled conformational space and flexibility differ significantly in both methods. Molecular dynamics simulations seem to better describe secondary structure content and identify regions responsible for conformational instability. The de novo method, as implemented in Rosetta-a prime tool for protein design, overestimates secondary structure content. On the other hand, its empirical energy function is capable to predict the threshold for protein stability.
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Affiliation(s)
- Keila C Cunha
- Department of Fundamental Chemistry, Federal University of Pernambuco, Recife, PE, 50740-560, Brazil
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9
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Kancherla AK, Meesala S, Jorwal P, Palanisamy R, Sikdar SK, Sarma SP. A Disulfide Stabilized β-Sandwich Defines the Structure of a New Cysteine Framework M-Superfamily Conotoxin. ACS Chem Biol 2015; 10:1847-60. [PMID: 25961405 DOI: 10.1021/acschembio.5b00226] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The structure of a new cysteine framework (-C-CC-C-C-C-) "M"-superfamily conotoxin, Mo3964, shows it to have a β-sandwich structure that is stabilized by inter-sheet cross disulfide bonds. Mo3964 decreases outward K(+) currents in rat dorsal root ganglion neurons and increases the reversal potential of the NaV1.2 channels. The structure of Mo3964 (PDB ID: 2MW7 ) is constructed from the disulfide connectivity pattern, i.e., 1-3, 2-5, and 4-6, that is hitherto undescribed for the "M"-superfamily conotoxins. The tertiary structural fold has not been described for any of the known conus peptides. NOE (549), dihedral angle (84), and hydrogen bond (28) restraints, obtained by measurement of (h3)JNC' scalar couplings, were used as input for structure calculation. The ensemble of structures showed a backbone root mean square deviation of 0.68 ± 0.18 Å, with 87% and 13% of the backbone dihedral (ϕ, ψ) angles lying in the most favored and additional allowed regions of the Ramachandran map. The conotoxin Mo3964 represents a new bioactive peptide fold that is stabilized by disulfide bonds and adds to the existing repertoire of scaffolds that can be used to design stable bioactive peptide molecules.
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Affiliation(s)
- Aswani K. Kancherla
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560012, India
| | - Srinu Meesala
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560012, India
| | - Pooja Jorwal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560012, India
| | - Ramasamy Palanisamy
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560012, India
| | - Sujit K. Sikdar
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560012, India
| | - Siddhartha P. Sarma
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560012, India
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10
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Kier BL, Anderson JM, Andersen NH. Disulfide-Mediated β-Strand Dimers: Hyperstable β-Sheets Lacking Tertiary Interactions and Turns. J Am Chem Soc 2015; 137:5363-71. [PMID: 25835058 PMCID: PMC7450586 DOI: 10.1021/ja5117809] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Disulfide bonds between cysteine residues are essential to the structure and folding of many proteins. Yet their role in the design of structured peptides and proteins has frequently been limited to use as intrachain covalent staples that reinforce existing structure or induce knot-like conformations. In β-hairpins, their placement at non-H-bonding positions across antiparallel strands has proven useful for achieving fully folded positive controls. Here we report a new class of designed β-sheet peptide dimers with strand-central disulfides as a key element. We have found that the mere presence of a disulfide bond near the middle of a short peptide chain is sufficient to nucleate some antiparallel β-sheet structure; addition of β-capping units and other favorable cross-strand interactions yield hyperstable sheets. Strand-central cystines were found to be superior to the best designed reversing turns in terms of nucleating β-sheet structure formation. We have explored the limitations and possibilities of this technique (the use of disulfides as sheet nucleators), and we provide a set of rules and rationales for the application and further design of disulfide-tethered "turnless" β-sheets.
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Affiliation(s)
- Brandon L Kier
- Chemistry Department, University of Washington, Seattle, Washington 98195, United States
| | - Jordan M Anderson
- Chemistry Department, University of Washington, Seattle, Washington 98195, United States
| | - Niels H Andersen
- Chemistry Department, University of Washington, Seattle, Washington 98195, United States
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11
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Haworth NL, Wouters MA. Cross-strand disulfides in the non-hydrogen bonding site of antiparallel β-sheet (aCSDns): poised for biological switching. RSC Adv 2015. [DOI: 10.1039/c5ra10672a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
aCSDns are forbidden disulfides with protein redox-activity. Within the aCSDn structural motif, a cognate substrate of Trx-like enzymes, the disulfide bonds are strained and metastable, facilitating their role as redox-regulated protein switches.
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Affiliation(s)
- Naomi L. Haworth
- Life and Environmental Sciences
- Deakin University
- Geelong 3217
- Australia
- Victor Chang Cardiac Research Institute
| | - Merridee A. Wouters
- Olivia Newton-John Cancer Research Institute
- Heidelberg 3084
- Australia
- School of Cancer Medicine
- La Trobe University
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12
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Kotamarthi HC, Narayan S, Ainavarapu SRK. Mechanical unfolding of ribose binding protein and its comparison with other periplasmic binding proteins. J Phys Chem B 2014; 118:11449-54. [PMID: 25216062 DOI: 10.1021/jp507463q] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Folding and unfolding studies on large, multidomain proteins are still rare despite their high abundance in genomes of prokaryotes and eukaryotes. Here, we investigate the unfolding properties of a 271 residue, two-domain ribose binding protein (RBP) from the bacterial periplasm using single-molecule force spectroscopy. We observe that RBP predominately unfolds via a two-state pathway with an unfolding force of ∼80 pN and an unfolding contour length of ∼95 nm. Only a small population (∼15%) of RBP follows three-state pathways. The ligand binding neither increases the mechanical stability nor influences the unfolding flux of RBP through different pathways. The kinetic partitioning between two-state and three-state pathways, which has been reported earlier for other periplasmic proteins, is also observed in RBP, albeit to a lesser extent. These results provide important insights into the mechanical stability and unfolding processes of large two-domain proteins and highlight the contrasting features upon ligand binding. Protein structural topology diagrams are used to explain the differences in the mechanical unfolding behavior of RBP with other periplasmic binding proteins.
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Affiliation(s)
- Hema Chandra Kotamarthi
- Department of Chemical Sciences, Tata Institute of Fundamental Research , Homi Bhabha Road, Colaba, Mumbai 400005, India
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Melnik TN, Majorina MA, Larina DS, Kashparov IA, Samatova EN, Glukhov AS, Melnik BS. Independent of their localization in protein the hydrophobic amino acid residues have no effect on the molten globule state of apomyoglobin and the disulfide bond on the surface of apomyoglobin stabilizes this intermediate state. PLoS One 2014; 9:e98645. [PMID: 24892675 PMCID: PMC4043776 DOI: 10.1371/journal.pone.0098645] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Accepted: 05/06/2014] [Indexed: 01/07/2023] Open
Abstract
At present it is unclear which interactions in proteins reveal the presence of intermediate states, their stability and formation rate. In this study, we have investigated the effect of substitutions of hydrophobic amino acid residues in the hydrophobic core of protein and on its surface on a molten globule type intermediate state of apomyoglobin. It has been found that independent of their localization in protein, substitutions of hydrophobic amino acid residues do not affect the stability of the molten globule state of apomyoglobin. It has been shown also that introduction of a disulfide bond on the protein surface can stabilize the molten globule state. However in the case of apomyoglobin, stabilization of the intermediate state leads to relative destabilization of the native state of apomyoglobin. The result obtained allows us not only to conclude which mutations can have an effect on the intermediate state of the molten globule type, but also explains why the introduction of a disulfide bond (which seems to “strengthen” the protein) can result in destabilization of the protein native state of apomyoglobin.
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Affiliation(s)
- Tatiana N. Melnik
- Institute of Protein Research, RAS, Pushchino, Moscow Region, Russia
| | - Maria A. Majorina
- Institute of Protein Research, RAS, Pushchino, Moscow Region, Russia
| | - Daria S. Larina
- Institute of Protein Research, RAS, Pushchino, Moscow Region, Russia
| | - Ivan A. Kashparov
- Institute of Protein Research, RAS, Pushchino, Moscow Region, Russia
| | - Ekaterina N. Samatova
- Institute of Protein Research, RAS, Pushchino, Moscow Region, Russia
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | | | - Bogdan S. Melnik
- Institute of Protein Research, RAS, Pushchino, Moscow Region, Russia
- * E-mail:
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The structured core domain of αB-crystallin can prevent amyloid fibrillation and associated toxicity. Proc Natl Acad Sci U S A 2014; 111:E1562-70. [PMID: 24711386 DOI: 10.1073/pnas.1322673111] [Citation(s) in RCA: 155] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mammalian small heat-shock proteins (sHSPs) are molecular chaperones that form polydisperse and dynamic complexes with target proteins, serving as a first line of defense in preventing their aggregation into either amorphous deposits or amyloid fibrils. Their apparently broad target specificity makes sHSPs attractive for investigating ways to tackle disorders of protein aggregation. The two most abundant sHSPs in human tissue are αB-crystallin (ABC) and HSP27; here we present high-resolution structures of their core domains (cABC, cHSP27), each in complex with a segment of their respective C-terminal regions. We find that both truncated proteins dimerize, and although this interface is labile in the case of cABC, in cHSP27 the dimer can be cross-linked by an intermonomer disulfide linkage. Using cHSP27 as a template, we have designed an equivalently locked cABC to enable us to investigate the functional role played by oligomerization, disordered N and C termini, subunit exchange, and variable dimer interfaces in ABC. We have assayed the ability of the different forms of ABC to prevent protein aggregation in vitro. Remarkably, we find that cABC has chaperone activity comparable to that of the full-length protein, even when monomer dissociation is restricted through disulfide linkage. Furthermore, cABC is a potent inhibitor of amyloid fibril formation and, by slowing the rate of its aggregation, effectively reduces the toxicity of amyloid-β peptide to cells. Overall we present a small chaperone unit together with its atomic coordinates that potentially enables the rational design of more effective chaperones and amyloid inhibitors.
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Góngora-Benítez M, Tulla-Puche J, Albericio F. Multifaceted Roles of Disulfide Bonds. Peptides as Therapeutics. Chem Rev 2013; 114:901-26. [DOI: 10.1021/cr400031z] [Citation(s) in RCA: 388] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Miriam Góngora-Benítez
- Institute
for Research in Biomedicine (IRB Barcelona), Barcelona, 08028 Spain
- CIBER-BBN, Barcelona Science
Park, Barcelona, 08028 Spain
| | - Judit Tulla-Puche
- Institute
for Research in Biomedicine (IRB Barcelona), Barcelona, 08028 Spain
- CIBER-BBN, Barcelona Science
Park, Barcelona, 08028 Spain
| | - Fernando Albericio
- Institute
for Research in Biomedicine (IRB Barcelona), Barcelona, 08028 Spain
- CIBER-BBN, Barcelona Science
Park, Barcelona, 08028 Spain
- Department
of Organic Chemistry, University of Barcelona, Barcelona, 08028 Spain
- School of Chemistry & Physics, University of KwaZulu-Natal, 4001 Durban, South Africa
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Yadahalli S, Gosavi S. Designing cooperativity into the designed protein Top7. Proteins 2013; 82:364-74. [PMID: 23966061 DOI: 10.1002/prot.24393] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 06/24/2013] [Accepted: 07/26/2013] [Indexed: 01/21/2023]
Abstract
The topology of the designed protein Top7 is not found in natural proteins. Top7 shows signatures of non-cooperative folding in both experimental studies and computer simulations. In particular, molecular dynamics of coarse-grained structure-based models of Top7 show a well-populated C-terminal folding-intermediate. Since most similarly sized globular proteins are cooperative folders, the non-natural topology of Top7 has been suggested as a reason for its non-cooperative folding. Here, we computationally examine the folding of Top7 with the intent of making it cooperative. We find that its folding cooperativity can be increased in two ways: (a) Optimization of packing interactions in the N-terminal half of the protein enables further folding of the C-terminal intermediate. (b) Reduction in the packing density of the C-terminal region destabilizes the intermediate. In practice, these strategies are implemented in our Top7 model through modifications to the contact-map. These modifications do not alter the topology of Top7 but result in cooperative folding. Amino-acid mutations that mimic these modifications also lead to a significant increase in folding cooperativity. Finally, we devise a method to randomize the sizes of amino-acids within the same topology, and confirm that the structure of Top7 makes its folding sensitive to packing interactions. In contrast, the ribosomal protein S6, which has secondary structure similar to Top7, has folding which is much less sensitive to packing perturbations. Thus, it should be possible to make a sequence fold cooperatively to the structure of Top7, but to do so its side-chain packing needs to be carefully designed.
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Affiliation(s)
- Shilpa Yadahalli
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, 560065, India; Manipal University, Madhav Nagar, Manipal, 576104, India
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Kotamarthi HC, Sharma R, Narayan S, Ray S, Ainavarapu SRK. Multiple Unfolding Pathways of Leucine Binding Protein (LBP) Probed by Single-Molecule Force Spectroscopy (SMFS). J Am Chem Soc 2013; 135:14768-74. [DOI: 10.1021/ja406238q] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hema Chandra Kotamarthi
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Riddhi Sharma
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Satya Narayan
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Sayoni Ray
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Sri Rama Koti Ainavarapu
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
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Comini MA, Krauth-Siegel RL, Bellanda M. Mono- and dithiol glutaredoxins in the trypanothione-based redox metabolism of pathogenic trypanosomes. Antioxid Redox Signal 2013; 19:708-22. [PMID: 22978520 PMCID: PMC3739957 DOI: 10.1089/ars.2012.4932] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
SIGNIFICANCE Glutaredoxins are ubiquitous small thiol proteins of the thioredoxin-fold superfamily. Two major groups are distinguished based on their active sites: the dithiol (2-C-Grxs) and the monothiol (1-C-Grxs) glutaredoxins with a CXXC and a CXXS active site motif, respectively. Glutaredoxins are involved in cellular redox and/or iron sulfur metabolism. Usually their functions are closely linked to the glutathione system. Trypanosomatids, the causative agents of several tropical diseases, rely on trypanothione as principal low molecular mass thiol, and their glutaredoxins readily react with the unique bis(glutathionyl) spermidine conjugate. RECENT ADVANCES Two 2-C-Grxs and three 1-C-Grxs have been identified in pathogenic trypanosomatids. The 2-C-Grxs catalyze the reduction of glutathione disulfide by trypanothione and display reductase activity towards protein disulfides, as well as protein-glutathione mixed disulfides. In vitro, all three 1-C-Grxs as well as the cytosolic 2-C-Grx of Trypanosoma brucei can complex an iron-sulfur cluster. Recently the structure of the 1-C-Grx1 has been solved by NMR spectroscopy. The structure is very similar to those of other 1-C-Grxs, with some differences in the loop containing the conserved cis-Pro and the surface charge distribution. CRITICAL ISSUES Although four of the five trypanosomal glutaredoxins proved to coordinate an iron-sulfur cluster in vitro, the physiological role of the mitochondrial and cytosolic proteins, respectively, has only started to be unraveled. FUTURE DIRECTIONS The use of trypanothione by the glutaredoxins has established a novel role for this parasite-specific dithiol. Future work should reveal if these differences can be exploited for the development of novel antiparasitic drugs.
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Affiliation(s)
- Marcelo A Comini
- Laboratory Redox Biology of Trypanosomes, Institut Pasteur de Montevideo, Montevideo, Uruguay.
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Madhongsa K, Pasan S, Phophetleb O, Nasompag S, Thammasirirak S, Daduang S, Taweechaisupapong S, Lomize AL, Patramanon R. Antimicrobial action of the cyclic peptide bactenecin on Burkholderia pseudomallei correlates with efficient membrane permeabilization. PLoS Negl Trop Dis 2013; 7:e2267. [PMID: 23785532 PMCID: PMC3681726 DOI: 10.1371/journal.pntd.0002267] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 05/01/2013] [Indexed: 01/05/2023] Open
Abstract
Burkholderia pseudomallei is a category B agent that causes Melioidosis, an acute and chronic disease with septicemia. The current treatment regimen is a heavy dose of antibiotics such as ceftazidime (CAZ); however, the risk of a relapse is possible. Peptide antibiotics are an alternative to classical antibiotics as they exhibit rapid action and are less likely to result in the development of resistance. The aim of this study was to determine the bactericidal activity against B. pseudomallei and examine the membrane disrupting abilities of the potent antimicrobial peptides: bactenecin, RTA3, BMAP-18 and CA-MA. All peptides exhibited >97% bactericidal activity at 20 µM, with bactenecin having slightly higher activity. Long term time-kill assays revealed a complete inhibition of cell growth at 50 µM bactenecin and CA-MA. All peptides inhibited biofilm formation comparable to CAZ, but exhibited faster kinetics (within 1 h). Bactenecin exhibited stronger binding to LPS and induced perturbation of the inner membrane of live cells. Interaction of bactenecin with model membranes resulted in changes in membrane fluidity and permeability, leading to leakage of dye across the membrane at levels two-fold greater than that of other peptides. Modeling of peptide binding on the membrane showed stable and deep insertion of bactenecin into the membrane (up to 9 Å). We propose that bactenecin is able to form dimers or large β-sheet structures in a concentration dependent manner and subsequently rapidly permeabilize the membrane, leading to cytosolic leakage and cell death in a shorter period of time compared to CAZ. Bactenecin might be considered as a potent antimicrobial agent for use against B. pseudomallei. Burkholderia pseudomallei is a category B agent that causes Melioidosis, an acute and chronic disease with septicemia. The current treatment regimen is a heavy dose of antibiotics such as ceftazidime (CAZ), however, the risk of a relapse is possible. In this study we demonstrate that bactenecin, CA-MA, RTA3 and BMAP-18 are able to inhibit the growth and biofilm formation of B. pseudomallei. The strong bactericidal activity of bactenecin is attributed to its greater ability to permeabilize the membrane. Computational modeling of these peptide-membrane interactions provide support for a model in which bactenecin is able to penetrate the membrane most effectively due to its cyclical structure. The peptide, bactenecin has the potential to act as a highly effective alternative to CAZ, or as a combination therapy with CAZ in the treatment of melioidosis. Furthermore, understanding the mechanism of bactenecin may help us better design more effective peptides therapeutics of choice for melioidosis.
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Affiliation(s)
- Kanjana Madhongsa
- Protein and Proteomics Research Center for Commercial and Industrial Purposes (ProCCI), Khon Kaen University, Khon Kaen, Thailand
- Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Supaluk Pasan
- Protein and Proteomics Research Center for Commercial and Industrial Purposes (ProCCI), Khon Kaen University, Khon Kaen, Thailand
- Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Onanong Phophetleb
- Protein and Proteomics Research Center for Commercial and Industrial Purposes (ProCCI), Khon Kaen University, Khon Kaen, Thailand
- Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Sawinee Nasompag
- Protein and Proteomics Research Center for Commercial and Industrial Purposes (ProCCI), Khon Kaen University, Khon Kaen, Thailand
- Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Sompong Thammasirirak
- Protein and Proteomics Research Center for Commercial and Industrial Purposes (ProCCI), Khon Kaen University, Khon Kaen, Thailand
- Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Sakda Daduang
- Protein and Proteomics Research Center for Commercial and Industrial Purposes (ProCCI), Khon Kaen University, Khon Kaen, Thailand
- Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Suwimol Taweechaisupapong
- Melioidosis Research Center, Khon Kaen University, Khon Kaen, Thailand
- Biofilm Research Group, Faculty of Dentistry, Khon Kaen University, Khon Kaen, Thailand
| | - Andrei L. Lomize
- College of Pharmacy, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Rina Patramanon
- Protein and Proteomics Research Center for Commercial and Industrial Purposes (ProCCI), Khon Kaen University, Khon Kaen, Thailand
- Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
- * E-mail:
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20
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Haworth NL, Wouters MA. Between-strand disulfides: forbidden disulfides linking adjacent β-strands. RSC Adv 2013. [DOI: 10.1039/c3ra42486c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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Van der Meeren R, Wen Y, Van Gelder P, Tommassen J, Devreese B, Savvides SN. New insights into the assembly of bacterial secretins: structural studies of the periplasmic domain of XcpQ from Pseudomonas aeruginosa. J Biol Chem 2012. [PMID: 23188826 DOI: 10.1074/jbc.m112.432096] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The type II secretion system is a multiprotein assembly spanning the inner and outer membranes in Gram-negative bacteria. It is found in almost all pathogenic bacteria where it contributes to virulence, host tissue colonization, and infection. The exoproteins are secreted across the outer membrane via a large translocation channel, the secretin, which typically adopts a dodecameric structure. These secretin channels have large periplasmic N-terminal domains that reach out into the periplasm for communication with the inner membrane platform and with a pseudopilus structure that spans the periplasm. Here we report the crystal structure of the N-terminal periplasmic domain of the secretin XcpQ from Pseudomonas aeruginosa, revealing a two-lobe dimeric assembly featuring parallel subunits engaging in well defined interactions at the tips of each lobe. We have employed structure-based engineering of disulfide bridges and native mass spectrometry to show that the periplasmic domain of XcpQ dimerizes in a concentration-dependent manner. Validation of these insights in the context of cellular full-length XcpQ and further evaluation of the functionality of disulfide-linked XcpQ establishes that the basic oligomerization unit of XcpQ is a dimer. This is consistent with the notion that the dodecameric secretin assembles as a hexamer of dimers to ensure correct projection of the N-terminal domains into the periplasm. Therefore, our studies provide a key conceptual advancement in understanding the assembly principles and dynamic function of type II secretion system secretins and challenge recent studies reporting monomers as the basic subunit of the secretin oligomer.
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Melnik BS, Povarnitsyna TV, Glukhov AS, Melnik TN, Uversky VN. SS-Stabilizing Proteins Rationally: Intrinsic Disorder-Based Design of Stabilizing Disulphide Bridges in GFP. J Biomol Struct Dyn 2012; 29:815-24. [DOI: 10.1080/07391102.2012.10507414] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Baranova E, Weeks S, Beelen S, Bukach O, Gusev N, Strelkov S. Three-Dimensional Structure of α-Crystallin Domain Dimers of Human Small Heat Shock Proteins HSPB1 and HSPB6. J Mol Biol 2011; 411:110-22. [DOI: 10.1016/j.jmb.2011.05.024] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Revised: 05/11/2011] [Accepted: 05/17/2011] [Indexed: 01/08/2023]
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Xie J, Qin M, Cao Y, Wang W. Mechanistic insight of photo-induced aggregation of chicken egg white lysozyme: the interplay between hydrophobic interactions and formation of intermolecular disulfide bonds. Proteins 2011; 79:2505-16. [PMID: 21661057 DOI: 10.1002/prot.23074] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Revised: 04/21/2011] [Accepted: 04/26/2011] [Indexed: 11/05/2022]
Abstract
Recently, it was reported that ultraviolet (UV) illumination could trigger the unfolding of proteins by disrupting the buried disulfide bonds. However, the consequence of such unfolding has not been adequately evaluated. Here, we report that unfolded chicken egg white lysozyme (CEWL) triggered by UV illumination can form uniform globular aggregates as confirmed by dynamic light scattering, atomic force microscopy, and transmission electron microscopy. The assembling process of such aggregates was also monitored by several other methods, such as circular dichroism, fluorescence spectroscopy, mass spectrometry based on chymotrypsin digestion, ANS-binding assay, Ellman essay, and SDS-PAGE. Our finding is that due to the dissociation of the native disulfide bonds by UV illumination, CEWL undergoes drastic conformational changes resulting in the exposure of some hydrophobic residues and free thiols. Subsequently, these partially unfolded molecules self-assemble into small granules driven by intermolecular hydrophobic interaction. With longer UV illumination or longer incubation time, these granules can further self-assemble into larger globular aggregates. The combined effects from both the hydrophobic interaction and the formation of intermolecular disulfide bonds dominate this process. Additionally, similar aggregation behavior can also be found in other three typical disulfide-bonded proteins, that is, α-lactalbumin, RNase A, and bovine serum albumin. Thus, we propose that such aggregation behavior might be a general mechanism for some disulfide-bonded proteins under UV irradiation.
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Affiliation(s)
- Jinbing Xie
- National Laboratory of Solid State Microstructure, Nanjing University, Nanjing, China
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