1
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Lin GH, Yu TA, Chang CF, Hsu CH. Proline Isomerization and Molten Globular Property of TgPDCD5 Secreted from Toxoplasma gondii Confers Its Regulation of Heparin Sulfate Binding. JACS AU 2024; 4:1763-1774. [PMID: 38818051 PMCID: PMC11134355 DOI: 10.1021/jacsau.3c00577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 03/08/2024] [Accepted: 03/11/2024] [Indexed: 06/01/2024]
Abstract
Toxoplasmosis, caused by Toxoplasma gondii, poses risks to vulnerable populations. TgPDCD5, a secreted protein of T. gondii, induces apoptosis through heparan sulfate-mediated endocytosis. The entry mechanism of TgPDCD5 has remained elusive. Here, we present the solution structure of TgPDCD5 as a helical bundle with an extended N-terminal helix, exhibiting molten globule characteristics. NMR perturbation studies reveal heparin/heparan sulfate binding involving the heparan sulfate/heparin proteoglycans-binding motif and the core region, influenced by proline isomerization of P107 residue. The heterogeneous proline recruits a cyclophilin TgCyp18, accelerating interconversion between conformers and regulating heparan/heparin binding. These atomic-level insights elucidate the binary switch's functionality, expose novel heparan sulfate-binding surfaces, and illuminate the unconventional cellular entry of pathogenic TgPDCD5.
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Affiliation(s)
- Gloria
Meng-Hsuan Lin
- Department
of Agricultural Chemistry, National Taiwan
University, Taipei 10617, Taiwan
- Genome
and Systems Biology Degree Program, National
Taiwan University and Academia Sinica, Taipei 10617, Taiwan
| | - Tsun-Ai Yu
- Genomic
Research Center, Academia Sinica, Taipei 115201, Taiwan
| | - Chi-Fon Chang
- Genomic
Research Center, Academia Sinica, Taipei 115201, Taiwan
| | - Chun-Hua Hsu
- Department
of Agricultural Chemistry, National Taiwan
University, Taipei 10617, Taiwan
- Genome
and Systems Biology Degree Program, National
Taiwan University and Academia Sinica, Taipei 10617, Taiwan
- Institute
of Biochemical Sciences, National Taiwan
University, Taipei 115201, Taiwan
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2
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Malard F, Sizun C, Thureau A, Carlier L, Lescop E. Structural transitions in TCTP tumor protein upon binding to the anti-apoptotic protein family member Mcl-1. J Biol Chem 2023:104830. [PMID: 37201583 PMCID: PMC10333598 DOI: 10.1016/j.jbc.2023.104830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 05/09/2023] [Accepted: 05/11/2023] [Indexed: 05/20/2023] Open
Abstract
Translationally Controlled Tumor Protein (TCTP) serves as a pro-survival factor in tumor cells, inhibiting the mitochondrial apoptosis pathway by enhancing the function of anti-apoptotic Bcl-2 family members Mcl-1 and Bcl-xL. TCTP specifically binds to Bcl-xL, preventing Bax-dependent Bcl-xL-induced cytochrome c release, and it reduces Mcl-1 turnover by inhibiting its ubiquitination, thereby decreasing Mcl-1-mediated apoptosis. TCTP harbors a BH3-like motif that forms a β-strand buried in the globular domain of the protein. In contrast, the crystal structure of the TCTP BH3-like peptide in complex with the Bcl-2 family member Bcl-xL reveals an α-helical conformation for the BH3-like motif, suggesting significant structural changes upon complex formation. Employing biochemical and biophysical methods, including limited proteolysis, circular dichroism NMR, and SAXS, we describe the TCTP complex with the Bcl-2 homolog Mcl-1. Our findings demonstrate that full-length TCTP binds to the BH3 binding groove of Mcl-1 via its BH3-like motif, experiencing conformational exchange at the interface on a micro- to milli-second timescale. Concurrently, the TCTP globular domain becomes destabilized, transitioning into a molten-globule state. Furthermore, we establish that the non-canonical residue D16 within TCTP BH3-like motif reduces stability while enhancing the dynamics of the intermolecular interface. In conclusion, we detail the structural plasticity of TCTP and discuss its implications for partner interactions and future anticancer drug design strategies aimed at targeting TCTP complexes.
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Affiliation(s)
- Florian Malard
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, LabEx LERMIT, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Christina Sizun
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, LabEx LERMIT, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | | | - Ludovic Carlier
- Laboratoire Des Biomolécules, LBM, Sorbonne Université, Ecole Normale Supérieure, PSL University, CNRS, Paris, France
| | - Ewen Lescop
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, LabEx LERMIT, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France.
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3
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Pro-inflammatory protein S100A9 alters membrane organization by dispersing ordered domains. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184113. [PMID: 36567033 DOI: 10.1016/j.bbamem.2022.184113] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 12/06/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022]
Abstract
Pro-inflammatory, calcium-binding protein S100A9 is localized in the cytoplasm of many cells and regulates several intracellular and extracellular processes. S100A9 is involved in neuroinflammation associated with the pathogenesis of Alzheimer's disease (AD). The number of studies on the impact of S100A9 in co-aggregation processes with amyloid-like proteins is increasing. However, there is still a lack of data on how this protein interacts with lipid membranes. We employed atomic force microscopy (AFM), dynamic light scattering (DLS), and fluorescence measurements (Laurdan and Thioflavin-T) to study the interaction between protein and the membrane surface. We used lipid vesicles in bulk and planar tethered lipid bilayers as biomimetic membrane models. We demonstrated that the protein accumulates on negatively charged lipid bilayers but with no further loss of the bilayer's integrity. The most important result is that the initial adsorption and accumulation of apo-form of S100A9 on the lipid membrane surface is lipid phase-sensitive. The breaking down of raft-like and disappearance of gel-like domains indicate that protein incorporates into the hydrophobic part of the lipid bilayer. We observed the most noticeable loss of integrity in lipid bilayers constructed from a lipid mixture (brain total lipid extract). Understanding the function and interactions of these proteins in cellular environments might expand the development of new diagnostic and therapeutic approaches for AD or other related diseases.
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4
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Gupta MN, Uversky VN. Pre-Molten, Wet, and Dry Molten Globules en Route to the Functional State of Proteins. Int J Mol Sci 2023; 24:ijms24032424. [PMID: 36768742 PMCID: PMC9916686 DOI: 10.3390/ijms24032424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/23/2023] [Accepted: 01/23/2023] [Indexed: 01/28/2023] Open
Abstract
Transitions between the unfolded and native states of the ordered globular proteins are accompanied by the accumulation of several intermediates, such as pre-molten globules, wet molten globules, and dry molten globules. Structurally equivalent conformations can serve as native functional states of intrinsically disordered proteins. This overview captures the characteristics and importance of these molten globules in both structured and intrinsically disordered proteins. It also discusses examples of engineered molten globules. The formation of these intermediates under conditions of macromolecular crowding and their interactions with nanomaterials are also reviewed.
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Affiliation(s)
- Munishwar Nath Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Hauz Khas, New Delhi 110016, India
| | - Vladimir N. Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- Correspondence: ; Tel.: +1-813-494-5816
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5
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Bhuvanachandra B, Sivaramakrishna D, Alim S, Swamy MJ, Podile AR. Deciphering the thermotolerance of chitinase O from Chitiniphilus shinanonensis by in vitro and in silico studies. Int J Biol Macromol 2022; 210:44-52. [PMID: 35537581 DOI: 10.1016/j.ijbiomac.2022.05.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 05/01/2022] [Accepted: 05/02/2022] [Indexed: 11/05/2022]
Abstract
Biochemical and biophysical studies revealed that chitinase O from Chitiniphilus shinanonensis (CsChiO) exhibits considerable thermotolerance, possibly due to the formation of a stable structural conformation. CsChiO is an exochitinase with a temperature optimum of 70 °C. The secondary structures of CsChiO and its catalytic domain (Cat-CsChiO) are only marginally affected upon heating up to 90 °C, as revealed by circular dichroism (CD) spectroscopy. Differential scanning calorimetric (DSC) studies revealed that CsChiO exhibits two endothermic transitions at ca. 51 °C (Tm1) and 59 °C (Tm2), whereas Cat-CsChiO shows a single endothermic transition at 52 °C. Together, the CD and DSC analyses suggested that the catalytic domain of CsChiO undergoes a thermotropic transition at ~52 °C from native state to another stable structural conformation. Results from molecular dynamic simulations corroborated that Cat-CsChiO adopts a stable structural conformation above 50 °C by partial unfolding. Thermotolerant CsChiO would be useful for the conversion of chitin, which is highly abundant, to biologically active COS. This study unveiled the adaptability of enzymes/proteins in nature to perform biological functions at elevated temperatures.
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Affiliation(s)
- Bhoopal Bhuvanachandra
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad 500 046, Telangana, India
| | - Dokku Sivaramakrishna
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad 500 046, Telangana, India
| | - Sk Alim
- School of Chemistry, University of Hyderabad, Gachibowli, Hyderabad 500 046, Telangana, India
| | - Musti J Swamy
- School of Chemistry, University of Hyderabad, Gachibowli, Hyderabad 500 046, Telangana, India
| | - Appa Rao Podile
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad 500 046, Telangana, India.
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6
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Evolutionary Conservation, Variability, and Adaptation of Type III Secretion Systems. J Membr Biol 2022; 255:599-612. [PMID: 35695900 DOI: 10.1007/s00232-022-00247-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 05/20/2022] [Indexed: 10/18/2022]
Abstract
Type III secretion (T3S) systems are complex bacterial structures used by many pathogens to inject proteins directly into the cytosol of the host cell. These secretion machines evolved from the bacterial flagella and they have been grouped into families by phylogenetic analysis. The T3S system is composed of more than 20 proteins grouped into five complexes: the cytosolic platform, the export apparatus, the basal body, the needle, and the translocon complex. While the proteins located inside the bacterium are conserved, those exposed to the external media present high variability among families. This suggests that the T3S systems have adapted to interact with different cells or tissues in the host, and/or have been subjected to the evolutionary pressure of the host immune defenses. Such adaptation led to changes in the sequence of the T3S needle tip and translocon suggesting differences in the mechanism of assembly and structure of this complex.
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7
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Katuwawala A, Zhao B, Kurgan L. DisoLipPred: accurate prediction of disordered lipid-binding residues in protein sequences with deep recurrent networks and transfer learning. Bioinformatics 2021; 38:115-124. [PMID: 34487138 DOI: 10.1093/bioinformatics/btab640] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 08/05/2021] [Accepted: 09/02/2021] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION Intrinsically disordered protein regions interact with proteins, nucleic acids and lipids. Regions that bind lipids are implicated in a wide spectrum of cellular functions and several human diseases. Motivated by the growing amount of experimental data for these interactions and lack of tools that can predict them from the protein sequence, we develop DisoLipPred, the first predictor of the disordered lipid-binding residues (DLBRs). RESULTS DisoLipPred relies on a deep bidirectional recurrent network that implements three innovative features: transfer learning, bypass module that sidesteps predictions for putative structured residues, and expanded inputs that cover physiochemical properties associated with the protein-lipid interactions. Ablation analysis shows that these features drive predictive quality of DisoLipPred. Tests on an independent test dataset and the yeast proteome reveal that DisoLipPred generates accurate results and that none of the related existing tools can be used to indirectly identify DLBR. We also show that DisoLipPred's predictions complement the results generated by predictors of the transmembrane regions. Altogether, we conclude that DisoLipPred provides high-quality predictions of DLBRs that complement the currently available methods. AVAILABILITY AND IMPLEMENTATION DisoLipPred's webserver is available at http://biomine.cs.vcu.edu/servers/DisoLipPred/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Akila Katuwawala
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Bi Zhao
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Lukasz Kurgan
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA 23284, USA
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8
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Sannigrahi A, Chattopadhyay K. Pore formation by pore forming membrane proteins towards infections. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 128:79-111. [PMID: 35034727 DOI: 10.1016/bs.apcsb.2021.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Over the last 25 years, the biology of membrane proteins, including the PFPs-membranes interactions is seeking attention for the development of successful drug molecules against a number of infectious diseases. Pore forming toxins (PFTs), the largest family of PFPs are considered as a group of virulence factors produced in a large number of pathogenic systems which include streptococcus, pneumonia, Staphylococcus aureus, E. coli, Mycobacterium tuberculosis, group A and B streptococci, Corynebacterium diphtheria and many more. PFTs are generally utilized by the disease causing pathogens to disrupt the host first line of defense i.e. host cell membranes through pore formation strategy. Although, pore formation is the principal mode of action of the PFTs but they can have additional adverse effects on the hosts including immune evasion. Recently, structural investigation of different PFTs have imparted the molecular mechanistic insights into how PFTs get transformed from its inactive state to active toxic state. On the basis of their structural entity, PFTs have been classified in different types and their mode of actions alters in terms of pore formation and corresponding cellular toxicity. Although pathogen genome analysis can identify the probable PFTs depending upon their structural diversity, there are so many PFTs which utilize the local environmental conditions to generate their pore forming ability using a novel strategy which is known as "conformational switch" of a protein. This conformational switch is considered as characteristics of the phase shifting proteins which were often utilized by many pathogenic systems to protect them from the invaders through allosteric communication between distant regions of the protein. In this chapter, we discuss the structure function relationships of PFTs and how activity of PFTs varies with the change in the environmental conditions has been explored. Finally, we demonstrate these structural insights to develop therapeutic potential to treat the infections caused by multidrug resistant pathogens.
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Affiliation(s)
- Achinta Sannigrahi
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru, Karnataka, India.
| | - Krishnananda Chattopadhyay
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, West Bengal, India.
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9
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Ultsch M, Holliday MJ, Gerhardy S, Moran P, Scales SJ, Gupta N, Oltrabella F, Chiu C, Fairbrother W, Eigenbrot C, Kirchhofer D. Structures of the ApoL1 and ApoL2 N-terminal domains reveal a non-classical four-helix bundle motif. Commun Biol 2021; 4:916. [PMID: 34316015 PMCID: PMC8316464 DOI: 10.1038/s42003-021-02387-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 06/23/2021] [Indexed: 02/07/2023] Open
Abstract
Apolipoprotein L1 (ApoL1) is a circulating innate immunity protein protecting against trypanosome infection. However, two ApoL1 coding variants are associated with a highly increased risk of chronic kidney disease. Here we present X-ray and NMR structures of the N-terminal domain (NTD) of ApoL1 and of its closest relative ApoL2. In both proteins, four of the five NTD helices form a four-helix core structure which is different from the classical four-helix bundle and from the pore-forming domain of colicin A. The reactivity with a conformation-specific antibody and structural models predict that this four-helix motif is also present in the NTDs of ApoL3 and ApoL4, suggesting related functions within the small ApoL family. The long helix 5 of ApoL1 is conformationally flexible and contains the BH3-like region. This BH3-like α-helix resembles true BH3 domains only in sequence and structure but not in function, since it does not bind to the pro-survival members of the Bcl-2 family, suggesting a Bcl-2-independent role in cytotoxicity. These findings should expedite a more comprehensive structural and functional understanding of the ApoL immune protein family.
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Affiliation(s)
- Mark Ultsch
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, USA
| | - Michael J Holliday
- Department of Early Discovery Biochemistry, Genentech Inc., South San Francisco, CA, USA
| | - Stefan Gerhardy
- Department of Early Discovery Biochemistry, Genentech Inc., South San Francisco, CA, USA
| | - Paul Moran
- Department of Early Discovery Biochemistry, Genentech Inc., South San Francisco, CA, USA
| | - Suzie J Scales
- Department of Immunology, Genentech Inc., South San Francisco, CA, USA
| | - Nidhi Gupta
- Department of Immunology, Genentech Inc., South San Francisco, CA, USA
| | | | - Cecilia Chiu
- Department of Antibody Engineering, Genentech Inc., South San Francisco, CA, USA
| | - Wayne Fairbrother
- Department of Early Discovery Biochemistry, Genentech Inc., South San Francisco, CA, USA
| | - Charles Eigenbrot
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, USA
| | - Daniel Kirchhofer
- Department of Early Discovery Biochemistry, Genentech Inc., South San Francisco, CA, USA.
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10
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Aberrant environment and PS-binding to calnuc C-terminal tail drives exosomal packaging and its metastatic ability. Biochem J 2021; 478:2265-2283. [PMID: 34047336 DOI: 10.1042/bcj20210016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 01/01/2023]
Abstract
The characteristic features of cancer cells are aberrant (acidic) intracellular pH and elevated levels of phosphatidylserine. The primary focus of cancer research is concentrated on the discovery of biomarkers directed towards early diagnosis and therapy. It has been observed that azoxymethane-treated mice demonstrate an increased expression of calnuc (a multi-domain, Ca2+- and DNA-binding protein) in their colon, suggesting it to be a good biomarker of carcinogenesis. We show that culture supernatants from tumor cells have significantly higher amounts of secreted calnuc compared to non-tumor cells, selectively packaged into exosomes. Exosomal calnuc is causal for epithelial-mesenchymal transition and atypical migration in non-tumor cells, which are key events in tumorigenesis and metastasis. In vitro studies reveal a significant affinity for calnuc towards phosphatidylserine, specifically to its C-terminal region, leading to the formation of 'molten globule' conformation. Similar structural changes are observed at acidic pH (pH 4), which demonstrates the role of the acidic microenvironment in causing the molten globule conformation and membrane interaction. On a precise note, we propose that the molten globule structure of calnuc caused by aberrant conditions in cancer cells to be the causative mechanism underlying its exosome-mediated secretion, thereby driving metastasis.
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11
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Di Rocco G, Bighi B, Borsari M, Bortolotti CA, Ranieri A, Sola M, Battistuzzi G. Electron Transfer and Electrocatalytic Properties of the Immobilized Met80Ala Cytochrome
c
Variant in Dimethylsulfoxide. ChemElectroChem 2021. [DOI: 10.1002/celc.202100499] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Giulia Di Rocco
- Department of Life Sciences University of Modena and Reggio Emilia via Campi 103 41125 Modena Italy
| | - Beatrice Bighi
- Department of Chemistry and Geology University of Modena and Reggio Emilia via Campi 103 41125 Modena Italy
| | - Marco Borsari
- Department of Chemistry and Geology University of Modena and Reggio Emilia via Campi 103 41125 Modena Italy
| | - Carlo Augusto Bortolotti
- Department of Life Sciences University of Modena and Reggio Emilia via Campi 103 41125 Modena Italy
| | - Antonio Ranieri
- Department of Life Sciences University of Modena and Reggio Emilia via Campi 103 41125 Modena Italy
| | - Marco Sola
- Department of Life Sciences University of Modena and Reggio Emilia via Campi 103 41125 Modena Italy
| | - Gianantonio Battistuzzi
- Department of Chemistry and Geology University of Modena and Reggio Emilia via Campi 103 41125 Modena Italy
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12
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Wang MM, Long GJ, Guo H, Liu XZ, Wang H, Dewer Y, Li ZQ, Liu K, Zhang QL, Ma YF, He P, He M. Two carboxylesterase genes in Plutella xylostella associated with sex pheromones and plant volatiles degradation. PEST MANAGEMENT SCIENCE 2021; 77:2737-2746. [PMID: 33527628 DOI: 10.1002/ps.6302] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/20/2021] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Carboxyl/cholinesterases (CCEs) are thought to play a pivotal role in the degradation of sex pheromones and plant-derived odorants in insects, but their exact biochemistry and physiological functions remain unclear. RESULTS In this study, two paralogous antennae-enriched CCEs from Plutella xylostella (PxylCCE16a and 16c) were identified and functionally characterized. High-purity protein preparations of active recombinant PxylCCE16a and 16c have been obtained from Sf9 insect cells by Ni2+ affinity purification. Our results revealed that the purified recombinant PxylCCE016c is able to degrade two sex pheromone components Z9-14:Ac and Z11-16:Ac at 27.64 ± 0.79% and 24.40 ± 3.07%, respectively, while PxylCCE016a presented relatively lower activity. Additionally, a similar difference in activity was measured in plant-derived odorants. Furthermore, both CCEs displayed obvious preferences for the two sex pheromone components, especially on Z11-16:Ac (Km values are in the range 7.82-45.06 μmol L-1 ) which much lower than plant odorants (Km values are in the range 1290-4030 μmol L-1 ). Furthermore, the activity of the two newly identified CCEs is pH-dependent. The activity at pH 6.5 is obviously higher than that at pH 5.0. Interestingly, only PxylCCE016c can be inhibited by a common esterase inhibitor triphenyl phosphate (TPP) with LC50 of 1570 ± 520 μmol L-1 . CONCLUSION PxylCCE16c plays a more essential role in odorant degradation than PxylCCE16a. Moreover, the current study provides novel potential pesticide targets for the notorious moth Plutella xylostella. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Mei-Mei Wang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, P. R. China
| | - Gui-Jun Long
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, P. R. China
| | - Huan Guo
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, P. R. China
| | - Xuan-Zheng Liu
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, P. R. China
| | - Hong Wang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, P. R. China
| | - Youssef Dewer
- Bioassay Research Department, Central Agricultural Pesticide Laboratory, Agricultural Research Center, Dokki, Giza, Egypt
| | - Zhao-Qun Li
- Key Laboratory of Tea Biology and Resource Utilization, Ministry of Agriculture, Tea Research Institute, Chinese Academy of Agricultural Science, Hangzhou, P. R. China
| | - Kun Liu
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, P. R. China
| | - Qiu-Liang Zhang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, P. R. China
| | - Yun-Feng Ma
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, P. R. China
| | - Peng He
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, P. R. China
| | - Ming He
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, P. R. China
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13
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Furukawa K, Aguirre C, So M, Sasahara K, Miyanoiri Y, Sakurai K, Yamaguchi K, Ikenaka K, Mochizuki H, Kardos J, Kawata Y, Goto Y. Isoelectric point-amyloid formation of α-synuclein extends the generality of the solubility and supersaturation-limited mechanism. Curr Res Struct Biol 2020; 2:35-44. [PMID: 34235468 PMCID: PMC8244297 DOI: 10.1016/j.crstbi.2020.03.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 03/02/2020] [Accepted: 03/30/2020] [Indexed: 12/30/2022] Open
Abstract
Proteins in either a native or denatured conformation often aggregate at an isoelectric point (pI), a phenomenon known as pI precipitation. However, only a few studies have addressed the role of pI precipitation in amyloid formation, the crystal-like aggregation of denatured proteins. We found that α-synuclein, an intrinsically disordered protein of 140 amino acid residues associated with Parkinson's disease, formed amyloid fibrils at pI (= 4.7) under the low-sodium phosphate conditions. Although α-synuclein also formed amyloid fibrils at a wide pH range under high concentrations of sodium phosphate, the pI-amyloid formation was characterized by marked amyloid-specific thioflavin T fluorescence and clear fibrillar morphology, indicating highly ordered structures. Analysis by heteronuclear NMR in combination with principal component analysis suggested that amyloid formation under low and high phosphate conditions occurred by distinct mechanisms. The former was likely to be caused by the intermolecular attractive charge-charge interactions, where α-synuclein has +17 and −17 charges even with the zero net charge. On the other hand, the latter was caused by the phosphate-dependent salting-out effects. pI-amyloid formation may play a role in the membrane-dependent amyloid formation of α-synuclein, where the negatively charged membrane surface reduces the local pH to pI and the membrane hydrophobic environment enhances electrostatic interactions. The results extend the supersaturation-limited mechanism of amyloid formation: Amyloid fibrils are formed under a variety of conditions of decreased solubility of denatured proteins triggered by the breakdown of supersaturation. pI precipitation of α-synuclein led to the formation of amyloid fibrils. Fibrils formed at pI were more organized than those formed under other conditions. Attractive charge-charge interactions are responsible for the pI-amyloid formation. pI-amyloid formation may lead to the amyloid formation upon phospholipid membranes.
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Affiliation(s)
- Koki Furukawa
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka, 565-0871, Japan
| | - Cesar Aguirre
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka, 565-0871, Japan
| | - Masatomo So
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka, 565-0871, Japan
| | - Kenji Sasahara
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka, 565-0871, Japan
| | - Yohei Miyanoiri
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka, 565-0871, Japan
| | - Kazumasa Sakurai
- Institute of Advanced Technology, Kindai University, Wakayama, 649-6493, Japan
| | - Keiichi Yamaguchi
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka, 565-0871, Japan
| | - Kensuke Ikenaka
- Department of Neurology, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita, Osaka, 565-0871, Japan
| | - Hideki Mochizuki
- Department of Neurology, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita, Osaka, 565-0871, Japan
| | - Jozsef Kardos
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Eötvös Loránd University, Pázmány P. Sétány 1/C, Budapest, 1117, Hungary
| | - Yasushi Kawata
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori, 680-8552, Japan
| | - Yuji Goto
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka, 565-0871, Japan
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14
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Agrawal DC, Yadav A, Khan MA, Kundu S, Kayastha AM. Denaturant Induced Equilibrium Unfolding and Conformational Transitional Studies of Germinated Fenugreek β-Amylase Revealed Molten Globule like State at Low pH. Protein Pept Lett 2020; 27:1046-1057. [PMID: 32242773 DOI: 10.2174/0929866527666200403082721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 02/22/2020] [Accepted: 02/24/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND β-Amylase (EC 3.2.1.2) is a maltogenic enzyme, which releases β-maltose from the non-reducing end of the substrates. The enzyme plays important roles for the production of vaccine, maltiol and maltose rich syrups. Apart from these applications the enzyme protects cells from abiotic as well as oxidative damage. The enzyme is βwell characterized in βplants and microbes and crystal structures of β-amylases βhave been βobtained from sweet potato, soybean and Bacillus cereus. OBJECTIVE Find out correlation between structural and functional stability induced by change in pH, temperature and chaotropes. METHODS Activity, intrinsic fluorescence, extrinsic fluorescence, near- and far- ultraviolet circular dichroism spectroscopic measurements were performed. RESULTS Peaks about 208 nm and 222 nm obtained by near-ultraviolet circular dichroism correspond to α-helix whereas peak at 215 nm shows presence of β-sheet. At pH 2.0, absence of tertiary structures, exposed of hydrophobic regions and presence of substantial secondary structures, revealed the existence of molten globule like state. Temperature induced denaturation studies showed that the enzyme was stable up to 75 ºC and the process was found to be irreversible in nature. Chaotropes dependent equilibrium unfolding studies revealed that at low concentration of chaotropes, ellipticity and intrinsic fluorescence βintensity were βdecreased βwhereas βenzymatic activity remained unchanged, which revealed fenugreek β-amylase is multi-domains enzyme and catalytic βdomain βis more βstable compare to non-catalytic domain. Moreover, the transition was sigmoidal and non-coincidental. CONCLUSION Results indicate the probable existence of intermediate states that might perform significant role in physiological process and biotechnological applications.
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Affiliation(s)
- Dinesh Chand Agrawal
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Anjali Yadav
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Mohd Asim Khan
- Department of Biochemistry, University of Delhi South Campus, New Delhi 110021, India
| | - Suman Kundu
- Department of Biochemistry, University of Delhi South Campus, New Delhi 110021, India
| | - Arvind M Kayastha
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, India
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15
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Huang Y, Soliakov A, Le Brun AP, Macdonald C, Johnson CL, Solovyova AS, Waller H, Moore GR, Lakey JH. Helix N-Cap Residues Drive the Acid Unfolding That Is Essential in the Action of the Toxin Colicin A. Biochemistry 2019; 58:4882-4892. [PMID: 31686499 PMCID: PMC6899464 DOI: 10.1021/acs.biochem.9b00705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/31/2019] [Indexed: 11/28/2022]
Abstract
Numerous bacterial toxins and other virulence factors use low pH as a trigger to convert from water-soluble to membrane-inserted states. In the case of colicins, the pore-forming domain of colicin A (ColA-P) has been shown both to undergo a clear acidic unfolding transition and to require acidic lipids in the cytoplasmic membrane, whereas its close homologue colicin N shows neither behavior. Compared to that of ColN-P, the ColA-P primary structure reveals the replacement of several uncharged residues with aspartyl residues, which upon replacement with alanine induce an unfolded state at neutral pH. Here we investigate ColA-P's structural requirement for these critical aspartyl residues that are largely situated at the N-termini of α helices. As previously shown in model peptides, the charged carboxylate side chain can act as a stabilizing helix N-Cap group by interacting with free amide hydrogen bond donors. Because this could explain ColA-P destabilization when the aspartyl residues are protonated or replaced with alanyl residues, we test the hypothesis by inserting asparagine, glutamine, and glutamate residues at these sites. We combine urea (fluorescence and circular dichroism) and thermal (circular dichroism and differential scanning calorimetry) denaturation experiments with 1H-15N heteronuclear single-quantum coherence nuclear magnetic resonance spectroscopy of ColA-P at different pH values to provide a comprehensive description of the unfolding process and confirm the N-Cap hypothesis. Furthermore, we reveal that, in urea, the single domain ColA-P unfolds in two steps; low pH destabilizes the first step and stabilizes the second.
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Affiliation(s)
- Yan Huang
- Institute
for Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle-upon-Tyne NE2 4HH, U.K.
- College
of Chemistry and Molecular Sciences, Wuhan
University, Wuhan 430072, People’s Republic of China
| | - Andrei Soliakov
- Institute
for Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle-upon-Tyne NE2 4HH, U.K.
| | - Anton P. Le Brun
- Institute
for Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle-upon-Tyne NE2 4HH, U.K.
- Australian
Centre for Neutron Scattering, Australian
Nuclear Science and Technology Organisation, Kirrawee DC, NSW 2232, Australia
| | - Colin Macdonald
- Department
of Chemistry Centre for Structural & Molecular Biology, School
of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K.
| | - Christopher L. Johnson
- Institute
for Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle-upon-Tyne NE2 4HH, U.K.
| | - Alexandra S. Solovyova
- Institute
for Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle-upon-Tyne NE2 4HH, U.K.
| | - Helen Waller
- Institute
for Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle-upon-Tyne NE2 4HH, U.K.
| | - Geoffrey R. Moore
- Department
of Chemistry Centre for Structural & Molecular Biology, School
of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K.
| | - Jeremy H. Lakey
- Institute
for Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle-upon-Tyne NE2 4HH, U.K.
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16
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Bartelli NL, Sun S, Gucinski GC, Zhou H, Song K, Hayes CS, Dahlquist FW. The Cytoplasm-Entry Domain of Antibacterial CdiA Is a Dynamic α-Helical Bundle with Disulfide-Dependent Structural Features. J Mol Biol 2019; 431:3203-3216. [PMID: 31181288 PMCID: PMC6727969 DOI: 10.1016/j.jmb.2019.05.049] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 05/01/2019] [Accepted: 05/30/2019] [Indexed: 01/04/2023]
Abstract
Many Gram-negative bacterial species use contact-dependent growth inhibition (CDI) systems to compete with neighboring cells. CDI+ strains express cell-surface CdiA effector proteins, which carry a toxic C-terminal region (CdiA-CT) that is cleaved from the effector upon transfer into the periplasm of target bacteria. The released CdiA-CT consists of two domains. The C-terminal domain is typically a nuclease that inhibits cell growth, and the N-terminal "cytoplasm-entry" domain mediates toxin translocation into the target-cell cytosol. Here, we use NMR and circular dichroism spectroscopic approaches to probe the structure, stability, and dynamics of the cytoplasm-entry domain from Escherichia coli STEC_MHI813. Chemical shift analysis reveals that the CdiA-CTMHI813 entry domain is composed of a C-terminal helical bundle and a dynamic N-terminal region containing two disulfide linkages. Disruption of the disulfides by mutagenesis or chemical reduction destabilizes secondary structure over the N-terminus, but has no effect on the C-terminal helices. Although critical for N-terminal structure, the disulfides have only modest effects on global thermodynamic stability, and the entry domain exhibits characteristics of a molten globule. We find that the disulfides form in vivo as the entry domain dwells in the periplasm of inhibitor cells prior to target-cell recognition. CdiA-CTMHI813 variants lacking either disulfide still kill target bacteria, but disruption of both bonds abrogates growth inhibition activity. We propose that the entry domain's dynamic structural features are critical for function. In its molten globule-like state, the domain resists degradation after delivery, yet remains pliable enough to unfold for membrane translocation.
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Affiliation(s)
- Nicholas L Bartelli
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106, United States
| | - Sheng Sun
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106, United States
| | - Grant C Gucinski
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, United States
| | - Hongjun Zhou
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106, United States
| | - Kiho Song
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106, United States
| | - Christopher S Hayes
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, United States; Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106, United States.
| | - Frederick W Dahlquist
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106, United States; Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, United States; Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106, United States.
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17
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Judy E, Kishore N. A look back at the molten globule state of proteins: thermodynamic aspects. Biophys Rev 2019; 11:365-375. [PMID: 31055760 PMCID: PMC6557940 DOI: 10.1007/s12551-019-00527-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 04/22/2019] [Indexed: 12/23/2022] Open
Abstract
Interest in protein folding intermediates lies in their significance to protein folding pathways. The molten globule (MG) state is one such intermediate lying on the kinetic (and sometimes thermodynamic) pathway between native and unfolded states. Development of our qualitative and quantitative understanding of the MG state can provide deeper insight into the folding pathways and hence potentially facilitate solution of the protein folding problem. An extensive look at literature suggests that most studies into protein MG states have been largely qualitative. Attempts to obtain quantitative insights into MG states have involved application of high-sensitivity calorimetry (differential scanning calorimetry and isothermal titration calorimetry). This review addresses the progress made in this direction by discussing the knowledge gained to date, along with the future promise of calorimetry, in providing quantitative information on the structural features of MG states. Particular attention is paid to the question of whether such states share common structural features or not. The difference in the nature of the transition from the MG state to the unfolded state, in terms of cooperativity, has also been addressed and discussed.
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Affiliation(s)
- Eva Judy
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400 076 India
| | - Nand Kishore
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400 076 India
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18
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Deryusheva E, Nemashkalova E, Galloux M, Richard C, Eléouët J, Kovacs D, Belle K, Tompa P, Uversky V, Permyakov S. Does Intrinsic Disorder in Proteins Favor Their Interaction with Lipids? Proteomics 2019; 19:e1800098. [DOI: 10.1002/pmic.201800098] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 12/09/2018] [Indexed: 02/06/2023]
Affiliation(s)
- Evgenia Deryusheva
- Russian Academy of SciencesInstitute for Biological Instrumentation Pushchino Moscow Region 142290 Russia
| | - Ekaterina Nemashkalova
- Russian Academy of SciencesInstitute for Biological Instrumentation Pushchino Moscow Region 142290 Russia
| | - Marie Galloux
- VIM, INRAUniversité Paris‐Saclay Jouy‐en‐Josas 78350 France
| | | | | | - Denis Kovacs
- VIB, Structural Biology Research CenterVrije Universiteit Brussel Brussels 1050 Belgium
| | - Karo Belle
- VIB, Structural Biology Research CenterVrije Universiteit Brussel Brussels 1050 Belgium
| | - Peter Tompa
- VIB, Structural Biology Research CenterVrije Universiteit Brussel Brussels 1050 Belgium
- Institute of EnzymologyResearch Centre for Natural Sciences of the Hungarian Academy of Sciences Budapest 1117 Hungary
| | - Vladimir Uversky
- Russian Academy of SciencesInstitute for Biological Instrumentation Pushchino Moscow Region 142290 Russia
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research InstituteMorsani College of MedicineUniversity of South Florida Tampa FL 33612 USA
| | - Sergei Permyakov
- Russian Academy of SciencesInstitute for Biological Instrumentation Pushchino Moscow Region 142290 Russia
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19
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Houwman JA, Westphal AH, Visser AJWG, Borst JW, van Mierlo CPM. Concurrent presence of on- and off-pathway folding intermediates of apoflavodoxin at physiological ionic strength. Phys Chem Chem Phys 2018; 20:7059-7072. [PMID: 29473921 DOI: 10.1039/c7cp07922b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Flavodoxins have a protein topology that can be traced back to the universal ancestor of the three kingdoms of life. Proteins with this type of architecture tend to temporarily misfold during unassisted folding to their native state and form intermediates. Several of these intermediate species are molten globules (MGs), which are characterized by a substantial amount of secondary structure, yet without the tertiary side-chain packing of natively folded proteins. An off-pathway MG is formed at physiological ionic strength in the case of the F44Y variant of Azotobacter vinelandii apoflavodoxin (i.e., flavodoxin without flavin mononucleotide (FMN)). Here, we show that at this condition actually two folding species of this apoprotein co-exist at equilibrium. These species were detected by using a combination of FMN fluorescence quenching upon cofactor binding to the apoprotein and of polarized time-resolved tryptophan fluorescence spectroscopy. Besides the off-pathway MG, we observe the simultaneous presence of an on-pathway folding intermediate, which is native-like. Presence of concurrent intermediates at physiological ionic strength enables future exploration of how aspects of the cellular environment, like for example involvement of chaperones, affect these species.
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Affiliation(s)
- Joseline A Houwman
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands.
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20
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Tang Y, Romano FB, Breña M, Heuck AP. The Pseudomonas aeruginosa type III secretion translocator PopB assists the insertion of the PopD translocator into host cell membranes. J Biol Chem 2018; 293:8982-8993. [PMID: 29685888 DOI: 10.1074/jbc.ra118.002766] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 04/10/2018] [Indexed: 11/06/2022] Open
Abstract
Many Gram-negative bacterial pathogens use a type III secretion system to infect eukaryotic cells. The injection of bacterial toxins or protein effectors via this system is accomplished through a plasma membrane channel formed by two bacterial proteins, termed translocators, whose assembly and membrane-insertion mechanisms are currently unclear. Here, using purified proteins we demonstrate that the translocators PopB and PopD in Pseudomonas aeruginosa assemble heterodimers in membranes, leading to stably inserted hetero-complexes. Using site-directed fluorescence labeling with an environment-sensitive probe, we found that hydrophobic segments in PopD anchor the translocator to the membrane, but without adopting a typical transmembrane orientation. A fluorescence dual-quenching assay revealed that the presence of PopB changes the conformation adopted by PopD segments in membranes. Furthermore, analysis of PopD's interaction with human cell membranes revealed that PopD adopts a distinctive conformation when PopB is present. An N-terminal region of PopD is only exposed to the host cytosol when PopB is present. We conclude that PopB assists with the proper insertion of PopD in cell membranes, required for the formation of a functional translocon and host infection.
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Affiliation(s)
- Yuzhou Tang
- From the Program in Molecular and Cellular Biology and
| | | | - Mariana Breña
- From the Program in Molecular and Cellular Biology and
| | - Alejandro P Heuck
- From the Program in Molecular and Cellular Biology and .,Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts 01003
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21
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Mansfield MJ, Doxey AC. Genomic insights into the evolution and ecology of botulinum neurotoxins. Pathog Dis 2018; 76:4978416. [PMID: 29684130 DOI: 10.1093/femspd/fty040] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 04/17/2018] [Indexed: 11/14/2022] Open
Affiliation(s)
- Michael J Mansfield
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
| | - Andrew C Doxey
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
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22
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Mondal AK, Sreekumar A, Kundu N, Kathuria R, Verma P, Gandhi S, Chattopadhyay K. Structural Basis and Functional Implications of the Membrane Pore-Formation Mechanisms of Bacterial Pore-Forming Toxins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1112:281-291. [DOI: 10.1007/978-981-13-3065-0_19] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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23
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Pirazzini M, Rossetto O, Eleopra R, Montecucco C. Botulinum Neurotoxins: Biology, Pharmacology, and Toxicology. Pharmacol Rev 2017; 69:200-235. [PMID: 28356439 PMCID: PMC5394922 DOI: 10.1124/pr.116.012658] [Citation(s) in RCA: 410] [Impact Index Per Article: 58.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The study of botulinum neurotoxins (BoNT) is rapidly progressing in many aspects.
Novel BoNTs are being discovered owing to next generation sequencing, but their
biologic and pharmacological properties remain largely unknown. The molecular
structure of the large protein complexes that the toxin forms with accessory
proteins, which are included in some BoNT type A1 and B1 pharmacological
preparations, have been determined. By far the largest effort has been dedicated to
the testing and validation of BoNTs as therapeutic agents in an ever increasing
number of applications, including pain therapy. BoNT type A1 has been also exploited
in a variety of cosmetic treatments, alone or in combination with other agents, and
this specific market has reached the size of the one dedicated to the treatment of
medical syndromes. The pharmacological properties and mode of action of BoNTs have
shed light on general principles of neuronal transport and protein-protein
interactions and are stimulating basic science studies. Moreover, the wide array of
BoNTs discovered and to be discovered and the production of recombinant BoNTs endowed
with specific properties suggest novel uses in therapeutics with increasing
disease/symptom specifity. These recent developments are reviewed here to provide an
updated picture of the biologic mechanism of action of BoNTs, of their increasing use
in pharmacology and in cosmetics, and of their toxicology.
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Affiliation(s)
- Marco Pirazzini
- Department of Biomedical Sciences, University of Padova, Italy (M.P., O.R., C.M.); Neurologic Department, University-Hospital S. Maria della Misericordia, Udine, Italy (R.E.); and Consiglio Nazionale delle Ricerche, Institute of Neuroscience, University of Padova, Italy (C.M.)
| | - Ornella Rossetto
- Department of Biomedical Sciences, University of Padova, Italy (M.P., O.R., C.M.); Neurologic Department, University-Hospital S. Maria della Misericordia, Udine, Italy (R.E.); and Consiglio Nazionale delle Ricerche, Institute of Neuroscience, University of Padova, Italy (C.M.)
| | - Roberto Eleopra
- Department of Biomedical Sciences, University of Padova, Italy (M.P., O.R., C.M.); Neurologic Department, University-Hospital S. Maria della Misericordia, Udine, Italy (R.E.); and Consiglio Nazionale delle Ricerche, Institute of Neuroscience, University of Padova, Italy (C.M.)
| | - Cesare Montecucco
- Department of Biomedical Sciences, University of Padova, Italy (M.P., O.R., C.M.); Neurologic Department, University-Hospital S. Maria della Misericordia, Udine, Italy (R.E.); and Consiglio Nazionale delle Ricerche, Institute of Neuroscience, University of Padova, Italy (C.M.)
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24
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Houwman JA, van Mierlo CPM. Folding of proteins with a flavodoxin-like architecture. FEBS J 2017; 284:3145-3167. [PMID: 28380286 DOI: 10.1111/febs.14077] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 03/13/2017] [Accepted: 04/03/2017] [Indexed: 12/21/2022]
Abstract
The flavodoxin-like fold is a protein architecture that can be traced back to the universal ancestor of the three kingdoms of life. Many proteins share this α-β parallel topology and hence it is highly relevant to illuminate how they fold. Here, we review experiments and simulations concerning the folding of flavodoxins and CheY-like proteins, which share the flavodoxin-like fold. These polypeptides tend to temporarily misfold during unassisted folding to their functionally active forms. This susceptibility to frustration is caused by the more rapid formation of an α-helix compared to a β-sheet, particularly when a parallel β-sheet is involved. As a result, flavodoxin-like proteins form intermediates that are off-pathway to native protein and several of these species are molten globules (MGs). Experiments suggest that the off-pathway species are of helical nature and that flavodoxin-like proteins have a nonconserved transition state that determines the rate of productive folding. Folding of flavodoxin from Azotobacter vinelandii has been investigated extensively, enabling a schematic construction of its folding energy landscape. It is the only flavodoxin-like protein of which cotranslational folding has been probed. New insights that emphasize differences between in vivo and in vitro folding energy landscapes are emerging: the ribosome modulates MG formation in nascent apoflavodoxin and forces this polypeptide toward the native state.
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Affiliation(s)
- Joseline A Houwman
- Laboratory of Biochemistry, Wageningen University and Research, The Netherlands
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25
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Bartolini A, Tempesti P, Resta C, Berti D, Smets J, Aouad YG, Baglioni P. Poly(ethylene glycol)-graft-poly(vinyl acetate) single-chain nanoparticles for the encapsulation of small molecules. Phys Chem Chem Phys 2017; 19:4553-4559. [DOI: 10.1039/c6cp07967a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Amphiphilic poly(ethylene glycol)-graft-poly(vinyl acetate) copolymers with a low degree of grafting undergo self-folding in water driven by hydrophobic interactions, resulting in single-chain nanoparticles (SCNPs) possessing a hydrodynamic radius of about 10 nm.
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Affiliation(s)
- Arianna Bartolini
- Department of Chemistry “Ugo Schiff” and CSGI
- University of Florence
- via della Lastruccia 3
- 50019 Florence
- Italy
| | - Paolo Tempesti
- Department of Chemistry “Ugo Schiff” and CSGI
- University of Florence
- via della Lastruccia 3
- 50019 Florence
- Italy
| | - Claudio Resta
- Department of Chemistry “Ugo Schiff” and CSGI
- University of Florence
- via della Lastruccia 3
- 50019 Florence
- Italy
| | - Debora Berti
- Department of Chemistry “Ugo Schiff” and CSGI
- University of Florence
- via della Lastruccia 3
- 50019 Florence
- Italy
| | - Johan Smets
- The Procter & Gamble Company
- 1853 Strombeek Bever
- Belgium
| | - Yousef G. Aouad
- The Procter & Gamble Company
- Winton Hill Technical Center 6100 Center Hill
- Cincinnati
- USA
| | - Piero Baglioni
- Department of Chemistry “Ugo Schiff” and CSGI
- University of Florence
- via della Lastruccia 3
- 50019 Florence
- Italy
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Houwman JA, André E, Westphal AH, van Berkel WJH, van Mierlo CPM. The Ribosome Restrains Molten Globule Formation in Stalled Nascent Flavodoxin. J Biol Chem 2016; 291:25911-25920. [PMID: 27784783 PMCID: PMC5207065 DOI: 10.1074/jbc.m116.756205] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 10/13/2016] [Indexed: 11/06/2022] Open
Abstract
Folding of proteins usually involves intermediates, of which an important type is the molten globule (MG). MGs are ensembles of interconverting conformers that contain (non-)native secondary structure and lack the tightly packed tertiary structure of natively folded globular proteins. Whereas MGs of various purified proteins have been probed to date, no data are available on their presence and/or effect during protein synthesis. To study whether MGs arise during translation, we use ribosome-nascent chain (RNC) complexes of the electron transfer protein flavodoxin. Full-length isolated flavodoxin, which contains a non-covalently bound flavin mononucleotide (FMN) as cofactor, acquires its native α/β parallel topology via a folding mechanism that contains an off-pathway intermediate with molten globular characteristics. Extensive population of this MG state occurs at physiological ionic strength for apoflavodoxin variant F44Y, in which a phenylalanine at position 44 is changed to a tyrosine. Here, we show for the first time that ascertaining the binding rate of FMN as a function of ionic strength can be used as a tool to determine the presence of the off-pathway MG on the ribosome. Application of this methodology to F44Y apoflavodoxin RNCs shows that at physiological ionic strength the ribosome influences formation of the off-pathway MG and forces the nascent chain toward the native state.
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Affiliation(s)
- Joseline A Houwman
- From the Laboratory of Biochemistry, Wageningen University, 6708 WE Wageningen, The Netherlands
| | - Estelle André
- From the Laboratory of Biochemistry, Wageningen University, 6708 WE Wageningen, The Netherlands
| | - Adrie H Westphal
- From the Laboratory of Biochemistry, Wageningen University, 6708 WE Wageningen, The Netherlands
| | - Willem J H van Berkel
- From the Laboratory of Biochemistry, Wageningen University, 6708 WE Wageningen, The Netherlands
| | - Carlo P M van Mierlo
- From the Laboratory of Biochemistry, Wageningen University, 6708 WE Wageningen, The Netherlands
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27
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Bhat V, Olenick MB, Schuchardt BJ, Mikles DC, McDonald CB, Farooq A. Molecular determinants of the binding specificity of BH3 ligands to BclXL apoptotic repressor. Biopolymers 2016; 101:573-82. [PMID: 24114183 DOI: 10.1002/bip.22419] [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: 06/19/2013] [Revised: 09/22/2013] [Accepted: 09/23/2013] [Indexed: 12/31/2022]
Abstract
B-cell lymphoma extra-large protein (BclXL) serves as an apoptotic repressor by virtue of its ability to recognize and bind to BH3 domains found within a diverse array of proapoptotic regulators. Herein, we investigate the molecular basis of the specificity of the binding of proapoptotic BH3 ligands to BclXL. Our data reveal that while the BH3 ligands harboring the LXXX[A/S]D and [R/Q]XLXXXGD motif bind to BclXL with high affinity in the submicromolar range, those with the LXXXGD motif afford weak interactions. This suggests that the presence of a glycine at the fourth position (G+4)--relative to the N-terminal leucine (L0) within the LXXXGD motif--mitigates binding, unless the LXXXGD motif also contains arginine/glutamine at the -2 position. Of particular note is the observation that the residues at the +4 and -2 positions within the LXXX[A/S]D and [R/Q]XLXXXGD motifs appear to be energetically coupled-replacement of either [A/S]+4 or [R/Q]-2 with other residues has little bearing on the binding affinity of BH3 ligands harboring one of these motifs. Collectively, our study lends new molecular insights into understanding the binding specificity of BH3 ligands to BclXL with important consequences on the design of novel anticancer drugs.
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Affiliation(s)
- Vikas Bhat
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136
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28
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Romano FB, Tang Y, Rossi KC, Monopoli KR, Ross JL, Heuck AP. Type 3 Secretion Translocators Spontaneously Assemble a Hexadecameric Transmembrane Complex. J Biol Chem 2016; 291:6304-15. [PMID: 26786106 DOI: 10.1074/jbc.m115.681031] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Indexed: 11/06/2022] Open
Abstract
A type 3 secretion system is used by many bacterial pathogens to inject proteins into eukaryotic cells. Pathogens insert a translocon complex into the target eukaryotic membrane by secreting two proteins known as translocators. How these translocators form a translocon in the lipid bilayer and why both proteins are required remains elusive. Pseudomonas aeruginosa translocators PopB and PopD insert pores into membranes forming homo- or hetero-complexes of undetermined stoichiometry. Single-molecule fluorescence photobleaching experiments revealed that PopD formed mostly hexameric structures in membranes, whereas PopB displayed a bi-modal distribution with 6 and 12 subunits peaks. However, individually the proteins are not functional for effector translocation. We have found that when added together, the translocators formed distinct hetero-complexes containing 8 PopB and 8 PopD molecules. Thus, the interaction between PopB and PopD guide the assembly of a unique hetero-oligomer in membranes.
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Affiliation(s)
| | - Yuzhou Tang
- From the Program in Molecular and Cellular Biology, and
| | - Kyle C Rossi
- the Departments of Biochemistry and Molecular Biology and
| | | | - Jennifer L Ross
- From the Program in Molecular and Cellular Biology, and Physics, University of Massachusetts, Amherst, Massachusetts 01003
| | - Alejandro P Heuck
- From the Program in Molecular and Cellular Biology, and the Departments of Biochemistry and Molecular Biology and
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29
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DeForte S, Uversky VN. Intrinsically disordered proteins in PubMed: what can the tip of the iceberg tell us about what lies below? RSC Adv 2016. [DOI: 10.1039/c5ra24866c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Papers that use IDP terminology represent only the tip of the iceberg of the larger body of literature on this subject.
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Affiliation(s)
- Shelly DeForte
- Department of Molecular Medicine
- Morsani College of Medicine
- University of South Florida
- Tampa
- USA
| | - Vladimir N. Uversky
- Department of Molecular Medicine
- Morsani College of Medicine
- University of South Florida
- Tampa
- USA
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30
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Kumar R, Sharma D, Jain R, Kumar S, Kumar R. Role of macromolecular crowding and salt ions on the structural-fluctuation of a highly compact configuration of carbonmonoxycytochrome c. Biophys Chem 2015; 207:61-73. [DOI: 10.1016/j.bpc.2015.09.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 09/04/2015] [Accepted: 09/06/2015] [Indexed: 11/25/2022]
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31
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Cosentino K, Ros U, García-Sáez AJ. Assembling the puzzle: Oligomerization of α-pore forming proteins in membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1858:457-466. [PMID: 26375417 DOI: 10.1016/j.bbamem.2015.09.013] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 08/26/2015] [Accepted: 09/09/2015] [Indexed: 12/21/2022]
Abstract
Pore forming proteins (PFPs) share the ability of creating pores that allow the passage of ions, proteins or other constituents through a wide variety of target membranes, ranging from bacteria to humans. They often cause cell death, as pore formation disrupts the membrane permeability barrier required for maintaining cell homeostasis. The organization into supramolecular complexes or oligomers that pierce the membrane is a common feature of PFPs. However, the molecular pathway of self-assembly and pore opening remains unclear. Here, we review the most recent discoveries in the mechanism of membrane oligomerization and pore formation of a subset of PFPs, the α-PFPs, whose pore-forming domains are formed by helical segments. Only now we are starting to grasp the molecular details of their function, mainly thanks to the introduction of single molecule microscopy and nanoscopy techniques. This article is part of a Special Issue entitled: Pore-forming toxins edited by Mauro Dalla Serra and Franco Gambale.
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Affiliation(s)
- Katia Cosentino
- Interfaculty Institute of Biochemistry (IFIB), University of Tübingen, Tübingen, Germany.,Max-Planck Institute for Intelligent Systems, Stuttgart, Germany
| | - Uris Ros
- Interfaculty Institute of Biochemistry (IFIB), University of Tübingen, Tübingen, Germany.,Max-Planck Institute for Intelligent Systems, Stuttgart, Germany.,Center for Protein Studies, Havana University, Havana, Cuba
| | - Ana J García-Sáez
- Interfaculty Institute of Biochemistry (IFIB), University of Tübingen, Tübingen, Germany.,Max-Planck Institute for Intelligent Systems, Stuttgart, Germany
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32
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He P, Zhang YN, Yang K, Li ZQ, Dong SL. An antenna-biased carboxylesterase is specifically active to plant volatiles in Spodoptera exigua. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2015; 123:93-100. [PMID: 26267057 DOI: 10.1016/j.pestbp.2015.03.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 03/20/2015] [Accepted: 03/20/2015] [Indexed: 06/04/2023]
Abstract
Odorant-degrading enzymes (ODEs) in sensillar lymph are proposed to play important roles in the maintenance of the sensitivity of the olfactory sensilla, by timely degrading the odorants that have already fulfilled the activation of the odorant receptor (OR). Here we reported the cloning and characterization of an ODE gene (SexiCXE10) from the polyphagous insect pest Spodoptera exigua. SexiCXE10 is a carboxylesterase (CXE) gene, encoding a protein with 538 amino acid residues, and bearing typical characteristics of Carboxyl/cholinesterase (CCE, EC 3.1.1.1.) gene family. Tissue-temporal expression pattern by qPCR revealed that the SexiCXE10 mRNA was highly antenna biased, and maintained at high level throughout the adult stage. Further fluorescence in situ hybridization demonstrated that SexiCXE10 mRNA signal was detected under sensilla basiconica and short and long sensilla trichodea. Finally, enzymatic study using purified recombinant enzyme showed that SexiCXE10 had high activity specifically for ester plant volatiles with 7-10 carbon atoms, while no activity was found with S. exigua sex pheromone components and plant volatiles with more carbon atoms. In addition, SexiCXE10 displayed lower activity at acidic pH (pH 5.0), while higher activity was found at neutral and alkaline conditions (pH 6.5-9.0). Our results suggest that SexiCXE10 may play an important role in the degradation of the host plant volatiles, and thus contributes to the high sensitivity of the olfactory system in S. exigua. Meanwhile, the CXE would be a potential target for developing behavioral antagonists and pesticides against S. exigua.
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Affiliation(s)
- Peng He
- Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Guizhou University, Ministry of Education, Guiyang 550025, China
| | - Ya-Nan Zhang
- Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; College of Life Sciences, Huaibei Normal University, Huaibei 235000, China
| | - Ke Yang
- Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhao-Qun Li
- Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuang-Lin Dong
- Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China.
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Chatterjee A, Caballero-Franco C, Bakker D, Totten S, Jardim A. Pore-forming Activity of the Escherichia coli Type III Secretion System Protein EspD. J Biol Chem 2015; 290:25579-94. [PMID: 26324713 DOI: 10.1074/jbc.m115.648204] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Indexed: 12/20/2022] Open
Abstract
Enterohemorrhagic Escherichia coli is a causative agent of gastrointestinal and diarrheal diseases. Pathogenesis associated with enterohemorrhagic E. coli involves direct delivery of virulence factors from the bacteria into epithelial cell cytosol via a syringe-like organelle known as the type III secretion system. The type III secretion system protein EspD is a critical factor required for formation of a translocation pore on the host cell membrane. Here, we show that recombinant EspD spontaneously integrates into large unilamellar vesicle (LUV) lipid bilayers; however, pore formation required incorporation of anionic phospholipids such as phosphatidylserine and an acidic pH. Leakage assays performed with fluorescent dextrans confirmed that EspD formed a structure with an inner diameter of ∼2.5 nm. Protease mapping indicated that the two transmembrane helical hairpin of EspD penetrated the lipid layer positioning the N- and C-terminal domains on the extralumenal surface of LUVs. Finally, a combination of glutaraldehyde cross-linking and rate zonal centrifugation suggested that EspD in LUV membranes forms an ∼280-320-kDa oligomeric structure consisting of ∼6-7 subunits.
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Affiliation(s)
- Abhishek Chatterjee
- From the Institute of Parasitology and Centre for Host-Parasite Interactions, McGill University, Ste-Anne-de-Bellevue, Québec H9X 3V9, Canada
| | - Celia Caballero-Franco
- From the Institute of Parasitology and Centre for Host-Parasite Interactions, McGill University, Ste-Anne-de-Bellevue, Québec H9X 3V9, Canada
| | - Dannika Bakker
- From the Institute of Parasitology and Centre for Host-Parasite Interactions, McGill University, Ste-Anne-de-Bellevue, Québec H9X 3V9, Canada
| | - Stephanie Totten
- From the Institute of Parasitology and Centre for Host-Parasite Interactions, McGill University, Ste-Anne-de-Bellevue, Québec H9X 3V9, Canada
| | - Armando Jardim
- From the Institute of Parasitology and Centre for Host-Parasite Interactions, McGill University, Ste-Anne-de-Bellevue, Québec H9X 3V9, Canada
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On the translocation of botulinum and tetanus neurotoxins across the membrane of acidic intracellular compartments. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1858:467-74. [PMID: 26307528 DOI: 10.1016/j.bbamem.2015.08.014] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 08/04/2015] [Accepted: 08/17/2015] [Indexed: 01/25/2023]
Abstract
Tetanus and botulinum neurotoxins are produced by anaerobic bacteria of the genus Clostridium and are the most poisonous toxins known, with 50% mouse lethal dose comprised within the range of 0.1-few nanograms per Kg, depending on the individual toxin. Botulinum neurotoxins are similarly toxic to humans and can therefore be considered for potential use in bioterrorism. At the same time, their neurospecificity and reversibility of action make them excellent therapeutics for a growing and heterogeneous number of human diseases that are characterized by a hyperactivity of peripheral nerve terminals. The complete crystallographic structure is available for some botulinum toxins, and reveals that they consist of four domains functionally related to the four steps of their mechanism of neuron intoxication: 1) binding to specific receptors of the presynaptic membrane; 2) internalization via endocytic vesicles; 3) translocation across the membrane of endocytic vesicles into the neuronal cytosol; 4) catalytic activity of the enzymatic moiety directed towards the SNARE proteins. Despite the many advances in understanding the structure-mechanism relationship of tetanus and botulinum neurotoxins, the molecular events involved in the translocation step have been only partially elucidated. Here we will review recent advances that have provided relevant insights on the process and discuss possible models that can be experimentally tested. This article is part of a Special Issue entitled: Pore-Forming Toxins edited by Mauro Dalla Serra and Franco Gambale.
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35
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Dar AA, Chat OA. Cosolubilization of Coumarin30 and Warfarin in Cationic, Anionic, and Nonionic Micelles: A Micelle–Water Interfacial Charge Dependent FRET. J Phys Chem B 2015; 119:11632-42. [DOI: 10.1021/jp511978h] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Aijaz Ahmad Dar
- Department of Chemistry, University of Kashmir, Srinagar-190006, Jammu and Kashmir India
| | - Oyais Ahmad Chat
- Department of Chemistry, University of Kashmir, Srinagar-190006, Jammu and Kashmir India
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36
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Crystal structure of the Ego1-Ego2-Ego3 complex and its role in promoting Rag GTPase-dependent TORC1 signaling. Cell Res 2015. [PMID: 26206314 DOI: 10.1038/cr.2015.86] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The target of rapamycin complex 1 (TORC1) integrates various hormonal and nutrient signals to regulate cell growth, proliferation, and differentiation. Amino acid-dependent activation of TORC1 is mediated via the yeast EGO complex (EGOC) consisting of Gtr1, Gtr2, Ego1, and Ego3. Here, we identify the previously uncharacterized Ycr075w-a/Ego2 protein as an additional EGOC component that is required for the integrity and localization of the heterodimeric Gtr1-Gtr2 GTPases, equivalent to mammalian Rag GTPases. We also report the crystal structure of the Ego1-Ego2-Ego3 ternary complex (EGO-TC) at 2.4 Å resolution, in which Ego2 and Ego3 form a heterodimer flanked along one side by Ego1. Structural data also reveal the structural conservation of protein components between the yeast EGO-TC and the human Ragulator, which acts as a GEF for Rag GTPases. Interestingly, however, artificial tethering of Gtr1-Gtr2 to the vacuolar membrane is sufficient to activate TORC1 in response to amino acids even in the absence of the EGO-TC. Our structural and functional data therefore support a model in which the EGO-TC acts as a scaffold for Rag GTPases in TORC1 signaling.
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37
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Thomas JL, Bose HS. Regulation of human 3-beta-hydroxysteroid dehydrogenase type-2 (3βHSD2) by molecular chaperones and the mitochondrial environment affects steroidogenesis. J Steroid Biochem Mol Biol 2015; 151:74-84. [PMID: 25448736 DOI: 10.1016/j.jsbmb.2014.11.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 10/09/2014] [Accepted: 11/19/2014] [Indexed: 10/24/2022]
Abstract
Human 3-β-hydroxysteroid dehydrogenase/isomerase types 1 and 2 (3βHSD1 and 3βHSD2, respectively) are expressed in a tissue-specific pattern by different genes. Site-directed mutagenesis studies have confirmed the function of the catalytic amino acids (Tyr154, Lys 158, Ser124 in both isoenzymes), substrate/inhibitor isoform-specific residues (His156 and Arg195 in 3βHSD1) and cofactor binding residues (Asp36 provides NAD(+) specificity in both isoenzymes). However, detailed analysis of isoform-specific organelle localization and characterization is difficult due to the 93% amino acid identity between the two isoforms. With recent advances in the knowledge of mitochondrial architecture and localization of the various translocases, our laboratory has studied the mechanisms regulating mitochondrial 3βHSD2 localization. The mitochondrial N-terminal leader sequence of 3βHSD2 directs its entry into the mitochondria where it is localized to the intermembrane space (IMS). Unlike other mitochondrial proteins, the N-terminal signal sequence of 3βHSD2 is not cleaved upon mitochondrial import. 3βHSD2 interacts with the mitochondrial translocase, Tim50, to regulate progesterone and androstenedione formation. Our studies suggest that its activity at the IMS is facilitated in a partially unfolded "molten globule" conformation by the proton pump between the matrix and IMS. The unfolded protein is refolded by the mitochondrial chaperones. The protons at the IMS are absorbed by the lipid vesicles, to maintain the proton pump and recycle 3βHSD2. As a result, one molecule of 3βHSD2 may participate in multiple catalytic reactions. In summary, the steroidogenic cell recycles 3βHSD2 to catalyze the reactions needed to produce androstenedione, progesterone and 17α-hydroxyprogesterone on demand in coordination with the mitochondrial translocase, Tim50. This article is part of a Special Issue entitled 'Steroid/Sterol signaling'.
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Affiliation(s)
- James L Thomas
- Division of Basic Medical Sciences, Mercer University School of Medicine, Macon, GA 31207, USA
| | - Himangshu S Bose
- Departments of Biochemistry, Biomedical Sciences, Mercer University School of Medicine, Savannah, GA 31404, USA; Memorial University Medical Center, Anderson Cancer Institute, Savannah, GA 31404, USA.
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Rosú SA, Rimoldi OJ, Prieto ED, Curto LM, Delfino JM, Ramella NA, Tricerri MA. Amyloidogenic propensity of a natural variant of human apolipoprotein A-I: stability and interaction with ligands. PLoS One 2015; 10:e0124946. [PMID: 25950566 PMCID: PMC4423886 DOI: 10.1371/journal.pone.0124946] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 03/19/2015] [Indexed: 12/18/2022] Open
Abstract
A number of naturally occurring mutations of human apolipoprotein A-I (apoA-I) have been associated with hereditary amyloidoses. The molecular mechanisms involved in amyloid-associated pathology remain largely unknown. Here we examined the effects of the Arg173Pro point mutation in apoA-I on the structure, stability, and aggregation propensity, as well as on the ability to bind to putative ligands. Our results indicate that the mutation induces a drastic loss of stability, and a lower efficiency to bind to phospholipid vesicles at physiological pH, which could determine the observed higher tendency to aggregate as pro-amyloidogenic complexes. Incubation under acidic conditions does not seem to induce significant desestabilization or aggregation tendency, neither does it contribute to the binding of the mutant to sodium dodecyl sulfate. While the binding to this detergent is higher for the mutant as compared to wt apoA-I, the interaction of the Arg173Pro variant with heparin depends on pH, being lower at pH 5.0 and higher than wt under physiological pH conditions. We suggest that binding to ligands as heparin or other glycosaminoglycans could be key events tuning the fine details of the interaction of apoA-I variants with the micro-environment, and probably eliciting the toxicity of these variants in hereditary amyloidoses.
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Affiliation(s)
- Silvana A. Rosú
- Instituto de Investigaciones Bioquímicas de La Plata (INIBIOLP), CONICET, La Plata, Buenos Aires, Argentina
- Facultad de Ciencias Médicas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - Omar J. Rimoldi
- Instituto de Investigaciones Bioquímicas de La Plata (INIBIOLP), CONICET, La Plata, Buenos Aires, Argentina
- Facultad de Ciencias Médicas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - Eduardo D. Prieto
- Instituto de Investigaciones Bioquímicas de La Plata (INIBIOLP), CONICET, La Plata, Buenos Aires, Argentina
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Universidad Nacional de La Plata-CONICET, La Plata, Buenos Aires, Argentina
| | - Lucrecia M. Curto
- Departamento de Química Biológica e Instituto de Bioquímica y Biofísica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - José M. Delfino
- Departamento de Química Biológica e Instituto de Bioquímica y Biofísica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Nahuel A. Ramella
- Instituto de Investigaciones Bioquímicas de La Plata (INIBIOLP), CONICET, La Plata, Buenos Aires, Argentina
- Facultad de Ciencias Médicas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - M. Alejandra Tricerri
- Instituto de Investigaciones Bioquímicas de La Plata (INIBIOLP), CONICET, La Plata, Buenos Aires, Argentina
- Facultad de Ciencias Médicas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
- * E-mail:
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Benke S, Roderer D, Wunderlich B, Nettels D, Glockshuber R, Schuler B. The assembly dynamics of the cytolytic pore toxin ClyA. Nat Commun 2015; 6:6198. [PMID: 25652783 PMCID: PMC4347018 DOI: 10.1038/ncomms7198] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 01/05/2015] [Indexed: 12/15/2022] Open
Abstract
Pore-forming toxins are protein assemblies used by many organisms to disrupt the membranes of target cells. They are expressed as soluble monomers that assemble spontaneously into multimeric pores. However, owing to their complexity, the assembly processes have not been resolved in detail for any pore-forming toxin. To determine the assembly mechanism for the ring-shaped, homododecameric pore of the bacterial cytolytic toxin ClyA, we collected a diverse set of kinetic data using single-molecule spectroscopy and complementary techniques on timescales from milliseconds to hours, and from picomolar to micromolar ClyA concentrations. The entire range of experimental results can be explained quantitatively by a surprisingly simple mechanism. First, addition of the detergent n-dodecyl-β-D-maltopyranoside to the soluble monomers triggers the formation of assembly-competent toxin subunits, accompanied by the transient formation of a molten-globule-like intermediate. Then, all sterically compatible oligomers contribute to assembly, which greatly enhances the efficiency of pore formation compared with simple monomer addition.
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Affiliation(s)
- Stephan Benke
- University of Zurich, Department of Biochemistry, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Daniel Roderer
- ETH Zurich, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, 8093 Zurich, Switzerland
| | - Bengt Wunderlich
- University of Zurich, Department of Biochemistry, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Daniel Nettels
- University of Zurich, Department of Biochemistry, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Rudi Glockshuber
- ETH Zurich, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, 8093 Zurich, Switzerland
| | - Benjamin Schuler
- University of Zurich, Department of Biochemistry, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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40
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Fauth EVF, Cilli EM, Ligabue-Braun R, Verli H. Differential effect of solution conditions on the conformation of the actinoporins Sticholysin II and Equinatoxin II. AN ACAD BRAS CIENC 2015; 86:1949-62. [PMID: 25590731 DOI: 10.1590/0001-3765201420140270] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 08/11/2014] [Indexed: 11/22/2022] Open
Abstract
Actinoporins are a family of pore-forming proteins with hemolytic activity. The structural basis for such activity appears to depend on their correct folding. Such folding encompasses a phosphocholine binding site, a tryptophan-rich region and the activity-related N-terminus segment. Additionally, different solution conditions are known to be able to influence the pore formation by actinoporins, as for Sticholysin II (StnII) and Equinatoxin II (EqtxII). In this context, the current work intends to characterize the influence of distinct solution conditions in the conformational behavior of these proteins through molecular dynamics (MD) simulations. The obtained data offer structural insights into actinoporins dynamics in solution, characterizing its conformational behavior at the atomic level, in accordance with previous experimental data on StnII and EqtxII hemolytic activities.
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Affiliation(s)
| | - Eduardo M Cilli
- Departamento de Bioquímica e Tecnologia Química, UNESP, Instituto de Química, Universidade Estadual Paulista, Araraquara, SP, Brasil
| | | | - Hugo Verli
- Centro de Biotecnologia, UFRGS, Porto Alegre, RS, Brasil
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41
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Naiyer A, Hassan MI, Islam A, Sundd M, Ahmad F. Structural characterization of MG and pre-MG states of proteins by MD simulations, NMR, and other techniques. J Biomol Struct Dyn 2015; 33:2267-84. [PMID: 25586676 DOI: 10.1080/07391102.2014.999354] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Almost all proteins fold via a number of partially structured intermediates such as molten globule (MG) and pre-molten globule states. Understanding the structure of these intermediates at atomic level is often a challenge, as these states are observed under extreme conditions of pH, temperature, and chemical denaturants. Furthermore, several other processes such as chemical modification, site-directed mutagenesis (or point mutation), and cleavage of covalent bond of natural proteins often lead to MG like partially unfolded conformation. However, the dynamic nature of proteins in these states makes them unsuitable for most structure determination at atomic level. Intermediate states studied so far have been characterized mostly by circular dichroism, fluorescence, viscosity, dynamic light scattering measurements, dye binding, infrared techniques, molecular dynamics simulations, etc. There is a limited amount of structural data available on these intermediate states by nuclear magnetic resonance (NMR) and hence there is a need to characterize these states at the molecular level. In this review, we present characterization of equilibrium intermediates by biophysical techniques with special reference to NMR.
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Affiliation(s)
- Abdullah Naiyer
- a Centre for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia , Jamia Nagar, New Delhi - 110025 , India
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42
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Bychkova VE, Basova LV, Balobanov VA. How membrane surface affects protein structure. BIOCHEMISTRY (MOSCOW) 2015; 79:1483-514. [DOI: 10.1134/s0006297914130045] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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43
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He P, Zhang YN, Li ZQ, Yang K, Zhu JY, Liu SJ, Dong SL. An antennae-enriched carboxylesterase from Spodoptera exigua displays degradation activity in both plant volatiles and female sex pheromones. INSECT MOLECULAR BIOLOGY 2014; 23:475-486. [PMID: 24628907 DOI: 10.1111/imb.12095] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Carboxyl/cholinesterase (CCE) is a large gene family of diverse functions, but in insects its function with respect to catabolism of sex pheromone components and plant volatiles is not well understood. In the present study, we cloned and functionally characterized one putative odorant-degrading enzyme (ODE) of the CCE family, SexiCXE14, from Spodoptera exigua. The tissue-temporal expression pattern revealed that the mRNA level of SexiCXE14 is antennae-enriched, sex equivalent and peaks at 3 days after moth eclosion. Functional study using the recombinant enzyme determined that SexiCXE14 has high degrading activity (Vmax) to host plant volatiles, suggesting its role in degradation of these volatiles. In addition, SexiCXE14 may also play a role in the degradation of sex pheromone components, as the Vmax and affinity parameter (Km) values with the sex pheromones are similar to those of reported pheromone degrading enzymes (PDEs). Further analysis of the relationship between substrate structure and enzymatic activity demonstrated that carbon chain length is a major influential factor, while the number of double bonds also affects the enzymatic activity. In addition, SexiCXE14 displays lower activity at acidic pH levels (pH 5.0) than in neutral conditions (pH 6.5). By characterizing this new ODE the present study provides insights in understanding of the high sensitivity of the moth olfactory system.
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Affiliation(s)
- P He
- Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing, China; State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Guizhou University, Ministry of Education, Guiyang, China
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44
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Rossetto O, Pirazzini M, Montecucco C. Botulinum neurotoxins: genetic, structural and mechanistic insights. Nat Rev Microbiol 2014; 12:535-49. [PMID: 24975322 DOI: 10.1038/nrmicro3295] [Citation(s) in RCA: 400] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Botulinum neurotoxins (BoNTs) are produced by anaerobic bacteria of the genus Clostridium and cause a persistent paralysis of peripheral nerve terminals, which is known as botulism. Neurotoxigenic clostridia belong to six phylogenetically distinct groups and produce more than 40 different BoNT types, which inactivate neurotransmitter release owing to their metalloprotease activity. In this Review, we discuss recent studies that have improved our understanding of the genetics and structure of BoNT complexes. We also describe recent insights into the mechanisms of BoNT entry into the general circulation, neuronal binding, membrane translocation and neuroparalysis.
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Affiliation(s)
- Ornella Rossetto
- 1] Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/B, 35131 Padova, Italy. [2] National Research Council Institute of Neuroscience, University of Padova, Via Ugo Bassi 58/B, 35131 Padova, Italy. [3]
| | - Marco Pirazzini
- 1] Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/B, 35131 Padova, Italy. [2] National Research Council Institute of Neuroscience, University of Padova, Via Ugo Bassi 58/B, 35131 Padova, Italy. [3]
| | - Cesare Montecucco
- 1] Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/B, 35131 Padova, Italy. [2] National Research Council Institute of Neuroscience, University of Padova, Via Ugo Bassi 58/B, 35131 Padova, Italy
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45
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Kudryashova E, Heisler D, Zywiec A, Kudryashov DS. Thermodynamic properties of the effector domains of MARTX toxins suggest their unfolding for translocation across the host membrane. Mol Microbiol 2014; 92:1056-71. [PMID: 24724536 DOI: 10.1111/mmi.12615] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/09/2014] [Indexed: 11/28/2022]
Abstract
MARTX (multifunctional autoprocessing repeats-in-toxin) family toxins are produced by Vibrio cholerae, Vibrio vulnificus, Aeromonas hydrophila and other Gram-negative bacteria. Effector domains of MARTX toxins cross the cytoplasmic membrane of a host cell through a putative pore formed by the toxin's glycine-rich repeats. The structure of the pore is unknown and the translocation mechanism of the effector domains is poorly understood. We examined the thermodynamic stability of the effector domains of V. cholerae and A. hydrophila MARTX toxins to elucidate the mechanism of their translocation. We found that all but one domain in each toxin are thermodynamically unstable and several acquire a molten globule state near human physiological temperatures. Fusion of the most stable cysteine protease domain to the adjacent effector domain reduces its thermodynamic stability ∼ 1.4-fold (from D G H 2 O 21.8 to 16.1 kJ mol(-1) ). Precipitation of several individual domains due to thermal denaturation is reduced upon their fusion into multi-domain constructs. We speculate that low thermostability of the MARTX effector domains correlates with that of many other membrane-penetrating toxins and implies their unfolding for cell entry. This study extends the list of thermolabile bacterial toxins, suggesting that this quality is essential and could be susceptible for selective targeting of pathogenic toxins.
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Affiliation(s)
- Elena Kudryashova
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
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46
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Bermejo IL, Arnulphi C, Ibáñez de Opakua A, Alonso-Mariño M, Goñi FM, Viguera AR. Membrane partitioning of the pore-forming domain of colicin A. Role of the hydrophobic helical hairpin. Biophys J 2014; 105:1432-43. [PMID: 24047995 DOI: 10.1016/j.bpj.2013.08.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 08/08/2013] [Accepted: 08/12/2013] [Indexed: 10/26/2022] Open
Abstract
The colicins are bacteriocins that target Escherichia coli and kill bacterial cells through different mechanisms. Colicin A forms ion channels in the inner membranes of nonimmune bacteria. This activity resides exclusively in its C-terminal fragment (residues 387-592). The soluble free form of this domain is a 10 α-helix bundle. The hydrophobic helical hairpin, H8-H9, is buried inside the structure and shielded by eight amphipathic surface helices. The interaction of the C-terminal colicin A domain and several chimeric variants with lipidic vesicles was examined here by isothermal titration calorimetry. In the mutant constructions, natural sequences of the hydrophobic helices H8 and H9 were either removed or substituted by polyalanine or polyleucine. All the constructions fully associated with DOPG liposomes including the mutant that lacked helices H8 and H9, indicating that amphipathic rather than hydrophobic helices were the major determinants of the exothermic binding reactions. Alanine is not specially favored in the lipid-bound form; the chimeric construct with polyalanine produced lower enthalpy gain. On the other hand, the large negative heat capacities associated with partitioning, a characteristic feature of the hydrophobic effect, were found to be dependent on the sequence hydrophobicity of helices H8 and H9.
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Affiliation(s)
- Ivan L Bermejo
- Unidad de Biofísica (CSIC, UPV/EHU), Barrio Sarriena s/n, Leioa, Spain
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47
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Bhat V, Olenick MB, Schuchardt BJ, Mikles DC, McDonald CB, Farooq A. Biophysical basis of the promiscuous binding of B-cell lymphoma protein 2 apoptotic repressor to BH3 ligands. J Mol Recognit 2014; 26:501-13. [PMID: 23996493 DOI: 10.1002/jmr.2295] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Revised: 06/25/2013] [Accepted: 06/26/2013] [Indexed: 01/09/2023]
Abstract
B-cell lymphoma protein 2 (Bcl2) apoptotic repressor carries out its function by virtue of its ability to bind to BH3 domains of various pro-apoptotic regulators in a highly promiscuous manner. Herein, we investigate the biophysical basis of such promiscuity of Bcl2 toward its cognate BH3 ligands. Our data show that although the BH3 ligands harboring the LXXXAD motif bind to Bcl2 with submicromolar affinity, those with the LXXX[G/S]D motif afford weak interactions. This implies that the replacement of alanine at the fourth position (A + 4)-relative to the N-terminal leucine (L0) within the LXXXAD motif-to glycine/serine results in the loss of free energy of binding. Consistent with this notion, the A + 4 residue within the BH3 ligands harboring the LXXXAD motif engages in key intermolecular van der Waals contacts with A149 lining the ligand binding groove within Bcl2, whereas A + 4G/S substitution results in the disruption of such favorable binding interactions. Of particular interest is the observation that although increasing ionic strength has little or negligible effect on the binding of high-affinity BH3 ligands harboring the LXXXAD motif, the binding of those with the LXXX[G/S]D motif in general experiences a varying degree of enhancement. This salient observation is indicative of the fact that hydrophobic forces not only play a dominant but also a universal role in driving the Bcl2-BH3 interactions. Taken together, our study sheds light on the molecular basis of the factors governing the promiscuous binding of Bcl2 to pro-apoptotic regulators and thus bears important consequences on the development of rational therapeutic approaches.
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Affiliation(s)
- Vikas Bhat
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
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48
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Selvakumar P, Sharma N, Tomar PPS, Kumar P, Sharma AK. Structural insights into the aggregation behavior of Murraya koenigii miraculin-like protein below pH 7.5. Proteins 2013; 82:830-40. [PMID: 24265134 DOI: 10.1002/prot.24461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Revised: 10/03/2013] [Accepted: 10/21/2013] [Indexed: 11/07/2022]
Abstract
Murraya koenigii miraculin-like protein (MKMLP) gradually precipitates below pH 7.5. Here, we explore the basis for this aggregation by identifying the aggregation-prone regions via comparative analysis of crystal structures acquired at several pH values. The prediction of aggregation-prone regions showed the presence of four short peptides either in beta sheets or loops on surface of the protein. These peptides were distributed in two patches far apart on the surface. Comparison of crystal structures of MKMLP, determined at 2.2 Å resolution in pH 7.0 and 4.6 in the present study and determined at 2.9 Å in pH 8.0 in an earlier reported study, reveal subtle conformational differences resulting in gradual exposure of aggregation-prone regions. As the pH is lowered, there are alterations in ionic interactions within the protein interactions of the chain with water molecules and exposure of hydrophobic residues. The analysis of symmetry-related molecular interfaces involving one patch revealed shortening of nonpolar intermolecular contacts as the pH decreased. In particular, a decrease in the intermolecular distance between Trp103 of the aggregation-prone peptide WFITTG (103-108) unique to MLPs was observed. These results demonstrated that aggregation occurs due to the cumulative effect of the changes in interactions in two aggregation-prone defined regions.
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Affiliation(s)
- Purushotham Selvakumar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247 667, India
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Pheromone discrimination by a pH-tuned polymorphism of the Bombyx mori pheromone-binding protein. Proc Natl Acad Sci U S A 2013; 110:18680-5. [PMID: 24158483 DOI: 10.1073/pnas.1317706110] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Bombyx mori pheromone-binding protein (BmorPBP) is known to adopt two different conformations. These are BmorPBP(A), where a regular helix formed by the C-terminal dodecapeptide segment, α7, occupies the ligand-binding cavity, and BmorPBP(B), where the binding site is free to accept ligands. NMR spectra of delipidated BmorPBP solutions at the physiological pH of the bulk sensillum lymph near pH 6.5 show only BmorPBP(A), and in mixtures, the two species are in slow exchange on the chemical shift frequency scale. This equilibrium has been monitored at variable pH and ligand concentrations, demonstrating that it is an intrinsic property of BmorPBP that is strongly affected by pH variation and ligand binding. This polymorphism tunes BmorPBP for optimal selective pheromone transport: Competition between α7 and lipophilic ligands for its binding cavity enables selective uptake of bombykol at the pore endings in the sensillum wall, whereas compounds with lower binding affinity can only be bound in the bulk sensillum lymph. After transport across the bulk sensillum lymph into the lower pH area near the dendritic membrane surface, bombykol is ejected near the receptor, whereas compounds with lower binding affinity are ejected before reaching the olfactory receptor, rendering them susceptible to degradation by enzymes present in the sensillum lymph.
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50
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Kumar TKS, Sivaraman T, Samuel D, Srisailam S, Ganesh G, Hsieh HC, Hung KW, Peng HJ, Ho MC, Arunkumar AI, Yu C. Protein Folding and β-Sheet Proteins. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.200000141] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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