901
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Tramontano A. The computational prediction of protein assemblies. Curr Opin Struct Biol 2017; 46:170-175. [PMID: 29102305 DOI: 10.1016/j.sbi.2017.10.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 10/04/2017] [Accepted: 10/05/2017] [Indexed: 10/18/2022]
Abstract
The function of proteins in the cell is almost always mediated by their interaction with different partners, including other proteins, nucleic acids or small organic molecules. The ability of identifying all of them is an essential step in our quest for understanding life at the molecular level. The inference of the protein complex composition and of its molecular details can also provide relevant clues for the development and the design of drugs. In this short review, I will discuss the computational aspects of the analysis and prediction of protein-protein assemblies and discuss some of the most recent developments as seen in the last Critical Assessment of Techniques for Protein Structure Prediction (CASP) experiment.
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Affiliation(s)
- Anna Tramontano
- Physics Department, Sapienza University of Rome, Piazzale Aldo Moro, 5 I-00185 Roma, Italy; Istituto Pasteur - Fondazione Cenci Bolognetti, Sapienza University of Rome, Piazzale Aldo Moro, 5 I-00185 Roma, Italy
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902
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Identification of small molecules uncoupling the Notch::Jagged interaction through an integrated high-throughput screening. PLoS One 2017; 12:e0182640. [PMID: 29099834 PMCID: PMC5669421 DOI: 10.1371/journal.pone.0182640] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 07/22/2017] [Indexed: 01/01/2023] Open
Abstract
Notch signaling plays an important role in several cellular functions including growth, differentiation, cell fate determination and stemness. Increased Notch activity has been linked to several types of cancers. Activation of Notch signaling is triggered by the interaction of Notch receptors (Notch1-4) with 5 different ligands (Jagged1-2 and Dll1-3-4) expressed on the neighbouring cells. Currently, indirect approaches to inhibit Notch signalling are based on the inhibition of the key step of Notch activation catalyzed by the γ-Secretase and thereby affect several different γ-Secretase substrates; conversely direct strategies get advantage of antibody-based drugs. The evidence that Jagged-mediated Notch activation plays a key role in cancer cell biology and the interplay with the surrounding microenvironment prompted us to develop a strategy to directly inhibit Notch activation by uncoupling its interaction with the Jagged, using an unprecedented approach based on small molecules. We set-up a screening strategy based on: protein::protein docking of crystallographic structures of Notch1 with Jagged1; comparative modelling of the Notch2:Jagged2 complex, based on the Notch1::Jagged1 complex; in silico high-throughput screening directed to Notch2 interaction surface of a virtual chemical library containing a large variety of molecules commercially available. The predicted pharmacological activity of the selected compounds was validated in vitro by a gene reporter and a viability assay. This approach led to the successful identification of two candidates with different anti-proliferative potency and efficacy. This represents the first step towards the rational identification of candidate molecules for the development of entirely novel drugs directed to inhibit Notch signaling in cancer.
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903
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Improved scFv Anti-LOX-1 Binding Activity by Fusion with LOX-1-Binding Peptides. BIOMED RESEARCH INTERNATIONAL 2017; 2017:8946935. [PMID: 29094051 PMCID: PMC5637825 DOI: 10.1155/2017/8946935] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 08/20/2017] [Indexed: 12/28/2022]
Abstract
The oxidized low-density lipoprotein receptor-1 (LOX-1) targeted single-chain variable fragment (scFvs) is a promising molecule for the targeted delivery of imaging and therapeutic molecules of atherosclerotic diseases; however, its applications are limited by the inherent low antigen affinity. In this study, the three-dimensional (3D) model of the anti-LOX-1 scFv was constructed and its docking with the LOX-1 protein was developed. To improve the LOX-1-binding activity, the anti-LOX-1 scFv was designed to fuse with one of three LOX-1-binding heptapeptides, LTPATAI, FQTPPQL, and LSIPPKA, at its N-terminus and C-terminus and in the linker region, which have different LOX-1-binding interfaces with the anti-LOX-1 scFv analyzed by an array of computational approaches. These scFv/peptide fusions were constructed, successfully expressed in Brevibacillus choshinensis hosts, and purified by a two-step column purification process. The antigen binding activity, structural characteristics, thermal stability, and stability in serum of these fusion proteins were examined. Results showed that the scFv with N-terminal fusing peptides proteins demonstrated increased LOX-1-binding activity without decrease in stability. These findings will help increase the application efficacy of LOX-1 targeting scFv in LOX-1-based therapy.
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904
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Jeong WH, Song DH, Hur GH, Jeong ST. Structure of the staphylococcal enterotoxin B vaccine candidate S19 showing eliminated superantigen activity. Acta Crystallogr F Struct Biol Commun 2017; 73:595-600. [PMID: 29095152 PMCID: PMC5683028 DOI: 10.1107/s2053230x17014844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 10/13/2017] [Indexed: 11/29/2022] Open
Abstract
Four mutations (N23A, Y90A, R110A and F177A) were introduced into S19, a vaccine candidate for staphylococcal enterotoxin B (SEB), resulting in a lower binding affinity towards the T-cell receptor beta chain (TCB) and reducing its superantigen activity. The structure of S19 was solved and was superposed on the native or complex structure of SEB. In the superposition model, mutations that were introduced seemed to reduce the number of hydrogen bonds at the SEB-TCB interface. S19 also displayed an unexpected structural change around the flexible-loop region owing to the Y90A mutation. This local structural change provided evidence that the mutated form of S19 could have a lower affinity for major histocompatibility complex (MHC) class II than wild-type SEB.
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Affiliation(s)
- Woo Hyeon Jeong
- The 5th R&D Institute, Agency for Defense Development, Yuseong PO Box 35, Yuseong-gu, Daejeon 34188, Republic of Korea
| | - Dong Hyun Song
- The 5th R&D Institute, Agency for Defense Development, Yuseong PO Box 35, Yuseong-gu, Daejeon 34188, Republic of Korea
| | - Gyeung Haeng Hur
- The 5th R&D Institute, Agency for Defense Development, Yuseong PO Box 35, Yuseong-gu, Daejeon 34188, Republic of Korea
| | - Seong Tae Jeong
- The 5th R&D Institute, Agency for Defense Development, Yuseong PO Box 35, Yuseong-gu, Daejeon 34188, Republic of Korea
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905
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Gencer S, Oleinik N, Kim J, Panneer Selvam S, De Palma R, Dany M, Nganga R, Thomas RJ, Senkal CE, Howe PH, Ogretmen B. TGF-β receptor I/II trafficking and signaling at primary cilia are inhibited by ceramide to attenuate cell migration and tumor metastasis. Sci Signal 2017; 10:eaam7464. [PMID: 29066540 PMCID: PMC5818989 DOI: 10.1126/scisignal.aam7464] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Signaling by the transforming growth factor-β (TGF-β) receptors I and II (TβRI/II) and the primary cilia-localized sonic hedgehog (Shh) pathway promote cell migration and, consequently, tumor metastasis. In contrast, the sphingolipid ceramide inhibits cell proliferation and tumor metastasis. We investigated whether ceramide metabolism inhibited TβRI/II trafficking to primary cilia to attenuate cross-talk between TβRI/II and the Shh pathway. We found that ceramide synthase 4 (CerS4)-generated ceramide stabilized the association between TβRI and the inhibitory factor Smad7, which limited the trafficking of TβRI/II to primary cilia. Expression of a mutant TβRI that signals but does not interact with Smad7 prevented the CerS4-mediated inhibition of migration in various cancer cells. Genetic deletion or knockdown of CerS4 prevented the formation of the Smad7-TβRI inhibitory complex and increased the association between TβRI and the transporter Arl6 through a previously unknown cilia-targeting signal (Ala31Thr32Ala33Leu34Gln35) in TβRI. Mutating the cilia-targeting signal abolished the trafficking of TβRI to the primary cilia. Localization of TβRI to primary cilia activated a key mediator of Shh signaling, Smoothened (Smo), which stimulated cellular migration and invasion. TβRI-Smo cross-talk at the cilia in CerS4-deficient 4T1 mammary cancer cells induced liver metastasis from orthotopic allografts in both wild-type and CerS4-deficient mice, which was prevented by overexpression of Smad7 or knockdown of intraflagellar transport protein 88 (IFT88). Overall, these data reveal a ceramide-dependent mechanism that suppresses cell migration and invasion by restricting TβRI/II-Shh signaling selectively at the plasma membrane of the primary cilium.
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Affiliation(s)
- Salih Gencer
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 125 Ashley Avenue, Charleston, SC 29425, USA
- Hollings Cancer Center, 86 Jonathan Lucas Street, Charleston, SC 29425, USA
| | - Natalia Oleinik
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 125 Ashley Avenue, Charleston, SC 29425, USA
- Hollings Cancer Center, 86 Jonathan Lucas Street, Charleston, SC 29425, USA
| | - Jisun Kim
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 125 Ashley Avenue, Charleston, SC 29425, USA
- Hollings Cancer Center, 86 Jonathan Lucas Street, Charleston, SC 29425, USA
| | - Shanmugam Panneer Selvam
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 125 Ashley Avenue, Charleston, SC 29425, USA
- Hollings Cancer Center, 86 Jonathan Lucas Street, Charleston, SC 29425, USA
| | - Ryan De Palma
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 125 Ashley Avenue, Charleston, SC 29425, USA
- Hollings Cancer Center, 86 Jonathan Lucas Street, Charleston, SC 29425, USA
| | - Mohammed Dany
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 125 Ashley Avenue, Charleston, SC 29425, USA
- Hollings Cancer Center, 86 Jonathan Lucas Street, Charleston, SC 29425, USA
| | - Rose Nganga
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 125 Ashley Avenue, Charleston, SC 29425, USA
- Hollings Cancer Center, 86 Jonathan Lucas Street, Charleston, SC 29425, USA
| | - Raquela J Thomas
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 125 Ashley Avenue, Charleston, SC 29425, USA
- Hollings Cancer Center, 86 Jonathan Lucas Street, Charleston, SC 29425, USA
| | - Can E Senkal
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 125 Ashley Avenue, Charleston, SC 29425, USA
- Hollings Cancer Center, 86 Jonathan Lucas Street, Charleston, SC 29425, USA
| | - Philip H Howe
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 125 Ashley Avenue, Charleston, SC 29425, USA
- Hollings Cancer Center, 86 Jonathan Lucas Street, Charleston, SC 29425, USA
| | - Besim Ogretmen
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 125 Ashley Avenue, Charleston, SC 29425, USA.
- Hollings Cancer Center, 86 Jonathan Lucas Street, Charleston, SC 29425, USA
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906
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Wadood A, Mehmood A, Khan H, Ilyas M, Ahmad A, Alarjah M, Abu-Izneid T. Epitopes based drug design for dengue virus envelope protein: A computational approach. Comput Biol Chem 2017; 71:152-160. [PMID: 29096381 DOI: 10.1016/j.compbiolchem.2017.10.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 10/04/2017] [Accepted: 10/19/2017] [Indexed: 12/25/2022]
Abstract
Dengue virus (DENV) has emerged as a rapidly spreading epidemic throughout the tropical and subtropical regions around the globe. No suitable drug has been designed yet to fight against DENV, therefore, the need for safe and effective antiviral drug has become imperative. The envelope protein of DENV is responsible for mediating the fusion process between viral and host membranes. This work reports an in silico approach to target B and T cell epitopes for dengue envelope protein inhibition. A conserved region "QHGTI" in B and T cell epitopes of dengue envelope glycoprotein was confirmed to be valid for targeting by visualizing its interactions with the host cell membrane TIM-1 protein which acts as a receptor for serotype 2 and 3. A reverse pharmacophore mapping approach was used to generate a seven featured pharmacophore model on the basis of predicted epitope. This pharmacophore model as a 3D query was used to virtually screen a chemical compounds dataset "Chembridge". A total of 1010 compounds mapped on the developed pharmacophore model. These retrieved hits were subjected to filtering via Lipinski's rule of five, as a result 442 molecules were shortlisted for further assessment using molecular docking. Finally, 14 hits of different structural properties having interactions with the active site residues of dengue envelope glycoprotein were selected as lead candidates. These structurally diverse lead candidates have strong likelihood to act as further starting structures in the development of novel and potential drugs for the treatment of dengue fever.
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Affiliation(s)
- Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan-23200, Pakistan.
| | - Aamir Mehmood
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan-23200, Pakistan
| | - Huma Khan
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan-23200, Pakistan
| | - Muhammad Ilyas
- Centre for Human Genetics, Hazara University, Mansehra, KP, Pakistan
| | - Ayaz Ahmad
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan-23200, Pakistan
| | - Mohammed Alarjah
- Pharmaceutical Chemistry Department, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Tareq Abu-Izneid
- Pharmaceutical Chemistry Department, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia.
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907
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Dequeker C, Laine E, Carbone A. INTerface Builder: A Fast Protein-Protein Interface Reconstruction Tool. J Chem Inf Model 2017; 57:2613-2617. [PMID: 28991473 DOI: 10.1021/acs.jcim.7b00360] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
INTerface Builder (INTBuilder) is a fast, easy-to-use program to compute protein-protein interfaces. It is designed to retrieve interfaces from molecular docking software outputs in an empirically determined linear complexity. INTBuilder directly reads the output formats of popular docking programs like ATTRACT, HEX, MAXDo, and ZDOCK, as well as a more generic format and Protein Data Bank (PDB) files. It identifies interacting surfaces at both residue and atom resolutions. INTerface Builder is an open source software written in C and freely available for noncommercial use (CeCILL license) at https://www.lcqb.upmc.fr/INTBuilder .
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Affiliation(s)
- Chloé Dequeker
- UPMC-Univ P6, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative-UMR 7238, Sorbonne Universités , 4 place Jussieu, 75005 Paris, France
| | - Elodie Laine
- UPMC-Univ P6, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative-UMR 7238, Sorbonne Universités , 4 place Jussieu, 75005 Paris, France
| | - Alessandra Carbone
- UPMC-Univ P6, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative-UMR 7238, Sorbonne Universités , 4 place Jussieu, 75005 Paris, France.,Institut Universitaire de France , Paris 75005, France
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908
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Schnicker NJ, Razzaghi M, Guha Thakurta S, Chakravarthy S, Dey M. Bacillus anthracis Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu. Biochemistry 2017; 56:5771-5785. [PMID: 28981257 DOI: 10.1021/acs.biochem.7b00601] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Prolyl hydroxylation is a very common post-translational modification and plays many roles in eukaryotes such as collagen stabilization, hypoxia sensing, and controlling protein transcription and translation. There is a growing body of evidence that suggests that prokaryotes contain prolyl 4-hydroxylases (P4Hs) homologous to the hypoxia-inducible factor (HIF) prolyl hydroxylase domain (PHD) enzymes that act on elongation factor Tu (EFTu) and are likely involved in the regulation of bacterial translation. Recent biochemical and structural studies with a PHD from Pseudomonas putida (PPHD) determined that it forms a complex with EFTu and hydroxylates a prolyl residue of EFTu. Moreover, while animal, plant, and viral P4Hs act on peptidyl proline, most prokaryotic P4Hs have been known to target free l-proline; the exceptions include PPHD and a P4H from Bacillus anthracis (BaP4H) that modifies collagen-like proline-rich peptides. Here we use biophysical and mass spectrometric methods to demonstrate that BaP4H recognizes full-length BaEFTu and a BaEFTu 9-mer peptide for site-specific proline hydroxylation. Using size-exclusion chromatography coupled small-angle X-ray scattering (SEC-SAXS) and binding studies, we determined that BaP4H forms a 1:1 heterodimeric complex with BaEFTu. The SEC-SAXS studies reveal dissociation of BaP4H dimeric subunits upon interaction with BaEFTu. While BaP4H is unusual within bacteria in that it is structurally and functionally similar to the animal PHDs and collagen P4Hs, respectively, this work provides further evidence of its promiscuous substrate recognition. It is possible that the enzyme might have evolved to hydroxylate a universally conserved protein in prokaryotes, similar to the PHDs, and implies a functional role in B. anthracis.
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Affiliation(s)
- Nicholas J Schnicker
- Department of Chemistry, The University of Iowa , Iowa City, Iowa 52242, United States
| | - Mortezaali Razzaghi
- Department of Chemistry, The University of Iowa , Iowa City, Iowa 52242, United States
| | - Sanjukta Guha Thakurta
- Department of Cell Biology, Harvard Medical School , 240 Longwood Avenue, Boston, Massachusetts 02115, United States
| | - Srinivas Chakravarthy
- Biophysics Collaborative Access Team, Argonne National Laboratory , Argonne, Illinois 60439, United States
| | - Mishtu Dey
- Department of Chemistry, The University of Iowa , Iowa City, Iowa 52242, United States
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909
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Berberich H, Terwesten F, Rakow S, Sahu P, Bouchard C, Meixner M, Philipsen S, Kolb P, Bauer UM. Identification and in silico structural analysis of Gallus gallus protein arginine methyltransferase 4 (PRMT4). FEBS Open Bio 2017; 7:1909-1923. [PMID: 29226078 PMCID: PMC5715347 DOI: 10.1002/2211-5463.12323] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 09/25/2017] [Indexed: 12/13/2022] Open
Abstract
Protein arginine methyltransferase 4 (PRMT4) is an essential epigenetic regulator of fundamental and conserved processes during vertebrate development, such as pluripotency and differentiation. Surprisingly, PRMT4 homologs have been identified in nearly all vertebrate classes except the avian genome. This raises the possibility that in birds PRMT4 functions are taken over by other PRMT family members. Here, we reveal the existence of a bona fidePRMT4 homolog in the chicken, Gallus gallus. Using a biochemical approach, we initially purified a putative chicken PRMT4 protein and thus provided the first evidence for the presence of an endogenous PRMT4‐specific enzymatic activity toward histone H3 arginine 17 (H3R17) in avian cells. We then isolated a G. gallus PRMT4 (ggPRMT4) transcript encompassing the complete open reading frame. Recombinant ggPRMT4 possesses intrinsic methyltransferase activity toward H3R17. CRISPR/Cas9‐mediated deletion of ggPRMT4 demonstrated that the transcript identified here encodes avian PRMT4. Combining protein–protein docking and homology modeling based on published crystal structures of murine PRMT4, we found a strong structural similarity of the catalytic core domain between chicken and mammalian PRMT4. Strikingly, in silico structural comparison of the N‐terminal Pleckstrin homology (PH) domain of avian and murine PRMT4 identified strictly conserved amino acids that are involved in an interaction interface toward the catalytic core domain, facilitating for the first time a prediction of the relative spatial arrangement of these two domains. Our novel findings are particularly exciting in light of the essential function of the PH domain in substrate recognition and methylation by PRMT4.
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Affiliation(s)
- Hannah Berberich
- Institute of Molecular Biology and Tumor Research (IMT) Philipps-University Marburg Germany
| | - Felix Terwesten
- Institute of Pharmaceutical Chemistry Philipps-University Marburg Germany
| | - Sinja Rakow
- Institute of Molecular Biology and Tumor Research (IMT) Philipps-University Marburg Germany
| | - Peeyush Sahu
- Institute of Molecular Biology and Tumor Research (IMT) Philipps-University Marburg Germany
| | - Caroline Bouchard
- Institute of Molecular Biology and Tumor Research (IMT) Philipps-University Marburg Germany
| | - Marion Meixner
- Institute of Molecular Biology and Tumor Research (IMT) Philipps-University Marburg Germany
| | - Sjaak Philipsen
- Department of Cell Biology Erasmus MC Rotterdam The Netherlands
| | - Peter Kolb
- Institute of Pharmaceutical Chemistry Philipps-University Marburg Germany
| | - Uta-Maria Bauer
- Institute of Molecular Biology and Tumor Research (IMT) Philipps-University Marburg Germany
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910
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Payandeh Z, Rajabibazl M, Mortazavi Y, Rahimpour A, Taromchi AH. Ofatumumab Monoclonal Antibody Affinity Maturation Through in silico Modeling. IRANIAN BIOMEDICAL JOURNAL 2017; 22:180-92. [PMID: 28992681 PMCID: PMC5889503 DOI: 10.22034/ibj.22.3.180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Background: Ofatumumab, an anti-CD20 mAb, was approved in 2009 for the treatment of chronic lymphocytic leukemia. This mAb acts through immune-mediated mechanisms, in particular complement-dependent cytotoxicity and antibody-dependent cellular cytotoxicity by natural killer cells as well as antibody-dependent phagocytosis by macrophages. Apoptosis induction is another mechanism of this antibody. Computational docking is the method of predicting the conformation of an antibody-antigen from its separated elements. Validation of the designed antibodies is carried out by docking tools. Increased affinity enhances the biological action of the antibody, which in turn improves the therapeutic effects. Furthermore, the increased antibody affinity can reduce the therapeutic dose of the antibody, resulting in lower toxicity and handling cost. Methods: Considering the importance of this issue, using in silico analysis such as docking and molecular dynamics, we aimed to find the important amino acids of the Ofatumumab antibody and then replaced these amino acids with others to improve antibody-binding affinity. Finally, we examined the binding affinity of antibody variants to antigen. Results: Our findings showed that variant 3 mutations have improved the characteristics of antibody binding compared to normal Ofatumumab antibodies. Conclusion: The designed anti-CD20 antibodies showed potentiality for improved affinity in comparison to commercial Ofatumumab.
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Affiliation(s)
- Zahra Payandeh
- Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Masoumeh Rajabibazl
- Department of Clinical Biochemistry, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Yousef Mortazavi
- Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran.,Cancer Gene Therapy Research Center, Faculty of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Azam Rahimpour
- School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amir Hossein Taromchi
- Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
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911
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Bhunia SS, Saxena AK. Molecular modelling studies in explaining the higher GPVI antagonistic activity of the racemic 2-(4-methoxyphenylsulfonyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxamide than its enantiomers. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2017; 28:783-799. [PMID: 29135287 DOI: 10.1080/1062936x.2017.1396247] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 10/20/2017] [Indexed: 06/07/2023]
Abstract
The GPVI receptor on the platelets plays a major role in inhibiting arterial thrombosis with limited risk of bleeding and is considered a potential anti-thrombotic target for arterial thrombosis. In the reported anti-thrombotics, tetrahydropyridoindoles, the title compound was the best inhibitor of the collagen mediated platelet aggregation by antagonizing the platelet receptor GPVI. Interestingly, the racemic title compound showed better antagonism (IC50 racemate = 6.7 μM) than either of its enantiomers (IC50 S enantiomer = 25.3 μM; IC50 R enantiomer = 126.3 μM). In order to explain this, the molecular modelling approaches viz. site map analysis, protein-protein docking and molecular dynamics simulation were carried out, which led to the identification of a second binding site located near the primary antagonist binding site known to bind losartan. The induced fit docking studies for both the enantiomers at the primary and secondary binding sites showed that the S-enantiomer has better interactions at the primary binding site than the R-enantiomer, while the R-enantiomer has better interactions at the secondary site than the S-enantiomer. Hence, the overall interactions of the racemic compound containing equimolar mixture may be higher than any one of the enantiomers and may explain the higher activity than its enantiomers of the racemic compound.
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Affiliation(s)
- S S Bhunia
- a Division of Medicinal and Process Chemistry , CSIR-Central Drug Research Institute , Lucknow , India
| | - A K Saxena
- a Division of Medicinal and Process Chemistry , CSIR-Central Drug Research Institute , Lucknow , India
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912
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Biogenic manganese oxide nanoparticle formation by a multimeric multicopper oxidase Mnx. Nat Commun 2017; 8:746. [PMID: 28963463 PMCID: PMC5622069 DOI: 10.1038/s41467-017-00896-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Accepted: 08/02/2017] [Indexed: 12/28/2022] Open
Abstract
Bacteria that produce Mn oxides are extraordinarily skilled engineers of nanomaterials that contribute significantly to global biogeochemical cycles. Their enzyme-based reaction mechanisms may be genetically tailored for environmental remediation applications or bioenergy production. However, significant challenges exist for structural characterization of the enzymes responsible for biomineralization. The active Mn oxidase in Bacillus sp. PL-12, Mnx, is a complex composed of a multicopper oxidase (MCO), MnxG, and two accessory proteins, MnxE and MnxF. MnxG shares sequence similarity with other, structurally characterized MCOs. MnxE and MnxF have no similarity to any characterized proteins. The ~200 kDa complex has been recalcitrant to crystallization, so its structure is unknown. Here, we show that native mass spectrometry defines the subunit topology and copper binding of Mnx, while high-resolution electron microscopy visualizes the protein and nascent Mn oxide minerals. These data provide critical structural information for understanding Mn biomineralization by such unexplored enzymes. Significant challenges exist for structural characterization of enzymes responsible for biomineralization. Here the authors show that native mass spectrometry and high resolution electron microscopy can define the subunit topology and copper binding of a manganese oxidizing complex, and describe early stage formation of its mineral products
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913
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Brandi V, Di Lella V, Marino M, Ascenzi P, Polticelli F. A comprehensive in silico analysis of huntingtin and its interactome. J Biomol Struct Dyn 2017; 36:3155-3171. [PMID: 28920551 DOI: 10.1080/07391102.2017.1381646] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A polyglutamine expansion of the N-terminal region of huntingtin (Htt) causes Huntington's disease, a severe neurodegenerative disorder. Htt huge multidomain structure, the presence of disordered regions, and the lack of sequence homologs of known structure, so far prevented structural studies of Htt, making the study of its structure-function relationships very difficult. In this work, the presence and location of five Htt ordered domains (named from Hunt1 to Hunt5) has been detected and the structure of these domains has been predicted for the first time using a combined threading/ab initio modeling approach. This work has led to the identification of a previously undetected HEAT repeats region in the Hunt3 domain. Furthermore, a putative function has been assigned to four out of the five domains. Hunt1 and Hunt5, displaying structural similarity with the regulatory subunit A of protein phosphatase 2A, are predicted to play a role in regulating the phosphorylation status of cellular proteins. Hunt2 and Hunt3 are predicted to be homologs of two yeast importins and to mediate vescicles transport and protein trafficking. Finally, a comprehensive analysis of the Htt interactome has been carried out and is discussed to provide a global picture of the Htt's structure-function relationships.
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Affiliation(s)
- Valentina Brandi
- a Department of Sciences , Roma Tre University, Viale Guglielmo Marconi 446 , Roma I-00146 , Italy
| | - Valentina Di Lella
- a Department of Sciences , Roma Tre University, Viale Guglielmo Marconi 446 , Roma I-00146 , Italy
| | - Maria Marino
- a Department of Sciences , Roma Tre University, Viale Guglielmo Marconi 446 , Roma I-00146 , Italy
| | - Paolo Ascenzi
- a Department of Sciences , Roma Tre University, Viale Guglielmo Marconi 446 , Roma I-00146 , Italy.,b Interdepartmental Laboratory for Electron Microscopy , Roma Tre University , Roma I-00146 , Italy
| | - Fabio Polticelli
- a Department of Sciences , Roma Tre University, Viale Guglielmo Marconi 446 , Roma I-00146 , Italy.,c National Institute of Nuclear Physics , Roma Tre University, Roma Tre Section , Roma I-00146 , Italy
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914
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Dai HS, Griffin N, Bolyard C, Mao HC, Zhang J, Cripe TP, Suenaga T, Arase H, Nakano I, Chiocca EA, Kaur B, Yu J, Caligiuri MA. The Fc Domain of Immunoglobulin Is Sufficient to Bridge NK Cells with Virally Infected Cells. Immunity 2017; 47:159-170.e10. [PMID: 28723548 DOI: 10.1016/j.immuni.2017.06.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 05/23/2017] [Accepted: 06/26/2017] [Indexed: 12/11/2022]
Abstract
Clearance of pathogens or tumor cells by antibodies traditionally requires both Fab and Fc domains of IgG. Here, we show the Fc domain of IgG alone mediates recognition and clearance of herpes simplex virus (HSV1)-infected cells. The human natural killer (NK) cell surface is naturally coated with IgG bound by its Fc domain to the Fcγ receptor CD16a. NK cells utilize the Fc domain of bound IgG to recognize gE, an HSV1-encoded glycoprotein that also binds the Fc domain of IgG but at a site distinct from CD16a. The bridge formed by the Fc domain between the HSV1-infected cell and the NK cell results in NK cell activation and lysis of the HSV1-infected cell in the absence of HSV1-specific antibody in vitro and prevents fatal HSV1 infection in vivo. This mechanism also explains how bacterial IgG-binding proteins regulate NK cell function and may be broadly applicable to Fcγ-receptor-bearing cells.
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Affiliation(s)
- Hong-Sheng Dai
- The Ohio State University Comprehensive Cancer Center, The James Cancer Hospital and Solove Research Institute, Columbus, OH 43210, USA; Division of Hematology, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, OH 43205, USA.
| | - Nathaniel Griffin
- The Ohio State University Comprehensive Cancer Center, The James Cancer Hospital and Solove Research Institute, Columbus, OH 43210, USA; Division of Hematology, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, OH 43205, USA
| | - Chelsea Bolyard
- Department of Neurological Surgery, The Ohio State University, Columbus, OH 43205, USA
| | - Hsiaoyin Charlene Mao
- The Ohio State University Comprehensive Cancer Center, The James Cancer Hospital and Solove Research Institute, Columbus, OH 43210, USA; Division of Hematology, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, OH 43205, USA
| | - Jianying Zhang
- Center for Biostatistics, The Ohio State University, Columbus, OH 43205, USA
| | - Timothy P Cripe
- Center for Childhood Cancer and Blood Diseases, Nationwide Children's Hospital, The Ohio State University, Columbus, OH 43205, USA; Division of Hematology/Oncology/Blood and Marrow Transplantation, Nationwide Children's Hospital, The Ohio State University, Columbus, OH 43205, USA
| | - Tadahiro Suenaga
- Laboratory of Immunochemistry, WPI Immunology Frontier Research Center and Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Hisashi Arase
- Laboratory of Immunochemistry, WPI Immunology Frontier Research Center and Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Ichiro Nakano
- Neurosurgery, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - E A Chiocca
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Balveen Kaur
- Department of Neurological Surgery, The Ohio State University, Columbus, OH 43205, USA
| | - Jianhua Yu
- The Ohio State University Comprehensive Cancer Center, The James Cancer Hospital and Solove Research Institute, Columbus, OH 43210, USA; Division of Hematology, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, OH 43205, USA
| | - Michael A Caligiuri
- The Ohio State University Comprehensive Cancer Center, The James Cancer Hospital and Solove Research Institute, Columbus, OH 43210, USA; Division of Hematology, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, OH 43205, USA.
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915
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Hakobyan D, Gerke V, Heuer A. Modeling of annexin A2-Membrane interactions by molecular dynamics simulations. PLoS One 2017; 12:e0185440. [PMID: 28937994 PMCID: PMC5609761 DOI: 10.1371/journal.pone.0185440] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 09/12/2017] [Indexed: 01/18/2023] Open
Abstract
The annexins are a family of Ca2+-regulated phospholipid binding proteins that are involved in membrane domain organization and membrane trafficking. Although they are widely studied and crystal structures are available for several soluble annexins their mode of membrane association has never been studied at the molecular level. Here we obtained molecular information on the annexin-membrane interaction that could serve as paradigm for the peripheral membrane association of cytosolic proteins by Molecular Dynamics simulations. We analyzed systems containing the monomeric annexin A2 (AnxA2), a membrane with negatively charged phosphatidylserine (POPS) lipids as well as Ca2+ ions. On the atomic level we identify the AnxA2 orientations and the respective residues which display the strongest interaction with Ca2+ ions and the membrane. The simulation results fully agree with earlier experimental findings concerning the positioning of bound Ca2+ ions. Furthermore, we identify for the first time a significant interaction between lysine residues of the protein and POPS lipids that occurs independently of Ca2+ suggesting that AnxA2-membrane interactions can also occur in a low Ca2+ environment. Finally, by varying Ca2+ concentrations and lipid composition in our simulations we observe a calcium-induced negative curvature of the membrane as well as an AnxA2-induced lipid ordering.
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Affiliation(s)
- Davit Hakobyan
- Institute of Physical Chemistry, University of Muenster, Muenster, Germany.,Center for Multiscale Theory and Computation (CMTC), University of Muenster, Muenster, Germany
| | - Volker Gerke
- Institute of Medical Biochemistry, Center of Molecular Biology of Inflammation (ZMBE), University of Muenster, Muenster, Germany
| | - Andreas Heuer
- Institute of Physical Chemistry, University of Muenster, Muenster, Germany.,Center for Multiscale Theory and Computation (CMTC), University of Muenster, Muenster, Germany
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916
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Deng B, Zhu S, Macklin AM, Xu J, Lento C, Sljoka A, Wilson DJ. Suppressing allostery in epitope mapping experiments using millisecond hydrogen / deuterium exchange mass spectrometry. MAbs 2017; 9:1327-1336. [PMID: 28933661 PMCID: PMC5680795 DOI: 10.1080/19420862.2017.1379641] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
Localization of the interface between the candidate antibody and its antigen target, commonly known as epitope mapping, is a critical component of the development of therapeutic monoclonal antibodies. With the recent availability of commercial automated systems, hydrogen / deuterium eXchange (HDX) is rapidly becoming the tool for mapping epitopes preferred by researchers in both industry and academia. However, this approach has a significant drawback in that it can be confounded by ‘allosteric’ structural and dynamic changes that result from the interaction, but occur far from the point(s) of contact. Here, we introduce a ‘kinetic’ millisecond HDX workflow that suppresses allosteric effects in epitope mapping experiments. The approach employs a previously introduced microfluidic apparatus that enables millisecond HDX labeling times with on-chip pepsin digestion and electrospray ionization. The ‘kinetic’ workflow also differs from conventional HDX-based epitope mapping in that the antibody is introduced to the antigen at the onset of HDX labeling. Using myoglobin / anti-myoglobin as a model system, we demonstrate that at short ‘kinetic’ workflow labeling times (i.e., 200 ms), the HDX signal is already fully developed at the ‘true’ epitope, but is still largely below the significance threshold at allosteric sites. Identification of the ‘true’ epitope is supported by computational docking predictions and allostery modeling using the rigidity transmission allostery algorithm.
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Affiliation(s)
- Bin Deng
- a Chemistry Department , York University , 4700 Keele Street, Toronto , ON , Canada.,b The Centre for Research in Mass Spectrometry , York University , Toronto , ON , Canada
| | - Shaolong Zhu
- a Chemistry Department , York University , 4700 Keele Street, Toronto , ON , Canada.,b The Centre for Research in Mass Spectrometry , York University , Toronto , ON , Canada
| | - Andrew M Macklin
- a Chemistry Department , York University , 4700 Keele Street, Toronto , ON , Canada.,b The Centre for Research in Mass Spectrometry , York University , Toronto , ON , Canada
| | - Jianrong Xu
- c Department of Pharmacology, Institute of Medical Sciences , Shanghai Jiao Tong University School of Medicine , Shanghai , P.R. China
| | - Cristina Lento
- a Chemistry Department , York University , 4700 Keele Street, Toronto , ON , Canada.,b The Centre for Research in Mass Spectrometry , York University , Toronto , ON , Canada
| | - Adnan Sljoka
- d Department of Informatics , Kwansei Gakuin University , Nishinomiya , Hyogo , Japan
| | - Derek J Wilson
- a Chemistry Department , York University , 4700 Keele Street, Toronto , ON , Canada.,b The Centre for Research in Mass Spectrometry , York University , Toronto , ON , Canada
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917
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Zanetti Polzi L, Battistuzzi G, Borsari M, Pignataro M, Paltrinieri L, Daidone I, Bortolotti CA. Computational investigation of the electron transfer complex between neuroglobin and cytochrome c. Supramol Chem 2017. [DOI: 10.1080/10610278.2017.1377342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Laura Zanetti Polzi
- Department of Physical and Chemical Sciences, University of L’Aquila, L’Aquila, Italy
| | - Gianantonio Battistuzzi
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Marco Borsari
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Marcello Pignataro
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Licia Paltrinieri
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Isabella Daidone
- Department of Physical and Chemical Sciences, University of L’Aquila, L’Aquila, Italy
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918
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Anashkina AA, Kravatsky Y, Kuznetsov E, Makarov AA, Adzhubei AA. Meta-server for automatic analysis, scoring and ranking of docking models. Bioinformatics 2017; 34:297-299. [PMID: 28968724 DOI: 10.1093/bioinformatics/btx591] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 07/28/2017] [Accepted: 09/15/2017] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Modelling with multiple servers that use different algorithms for docking results in more reliable predictions of interaction sites. However, the scoring and comparison of all models by an expert is time-consuming and is not feasible for large volumes of data generated by such modelling. RESULTS Quality ASsessment of DOcking Models (QASDOM) Server is a simple and efficient tool for real-time simultaneous analysis, scoring and ranking of data sets of receptor-ligand complexes built by a range of docking techniques. This meta-server is designed to analyse large data sets of docking models and rank them by scoring criteria developed in this study. It produces two types of output showing the likelihood of specific residues and clusters of residues to be involved in receptor-ligand interactions and the ranking of models. The server also allows visualizing residues that form interaction sites in the receptor and ligand sequence and displays 3D model structures of the receptor-ligand complexes. AVAILABILITY http://qasdom.eimb.ru. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Anastasia A Anashkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Yuri Kravatsky
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Eugene Kuznetsov
- V. A. Trapeznikov Institute of Control Sciences of Russian Academy of Sciences, Moscow, Russia
| | - Alexander A Makarov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexei A Adzhubei
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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919
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Tumor Inhibitory Effect of IRCR201, a Novel Cross-Reactive c-Met Antibody Targeting the PSI Domain. Int J Mol Sci 2017; 18:ijms18091968. [PMID: 28902178 PMCID: PMC5618617 DOI: 10.3390/ijms18091968] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 09/01/2017] [Accepted: 09/08/2017] [Indexed: 01/03/2023] Open
Abstract
Hepatocyte growth factor receptor (HGFR, c-Met) is an essential member of the receptor tyrosine kinase (RTK) family that is often dysregulated during tumor progression, driving a malignant phenotypic state and modulating important cellular functions including tumor growth, invasion, metastasis, and angiogenesis, providing a strong rationale for targeting HGF/c-Met signaling axis in cancer therapy. Based on its protumorigenic potentials, we developed IRCR201, a potent antagonistic antibody targeting the plexin-semaphorin-integrin (PSI) domain of c-Met, using synthetic human antibody phage libraries. We characterized and evaluated the biochemical properties and tumor inhibitory effect of IRCR201 in vitro and in vivo. IRCR201 is a novel fully-human bivalent therapeutic antibody that exhibits cross-reactivity against both human and mouse c-Met proteins with high affinity and specificity. IRCR201 displayed low agonist activity and rapidly depleted total c-Met protein via the lysosomal degradation pathway, inhibiting c-Met-dependent downstream activation and attenuating cellular proliferation in various c-Met-expressing cancer cells. In vivo tumor xenograft models also demonstrated the superior tumor inhibitory responsiveness of IRCR201. Taken together, IRCR201 provides a promising therapeutic agent for c-Met-positive cancer patients through suppressing the c-Met signaling pathway and tumor growth.
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920
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MinD directly interacting with FtsZ at the H10 helix suggests a model for robust activation of MinC to destabilize FtsZ polymers. Biochem J 2017; 474:3189-3205. [PMID: 28743721 DOI: 10.1042/bcj20170357] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 07/10/2017] [Accepted: 07/25/2017] [Indexed: 12/30/2022]
Abstract
Cell division in bacteria is a highly controlled and regulated process. FtsZ, a bacterial cytoskeletal protein, forms a ring-like structure known as the Z-ring and recruits more than a dozen other cell division proteins. The Min system oscillates between the poles and inhibits the Z-ring formation at the poles by perturbing FtsZ assembly. This leads to an increase in the FtsZ concentration at the mid-cell and helps in Z-ring positioning. MinC, the effector protein, interferes with Z-ring formation through two different mechanisms mediated by its two domains with the help of MinD. However, the mechanism by which MinD triggers MinC activity is not yet known. We showed that MinD directly interacts with FtsZ with an affinity stronger than the reported MinC-FtsZ interaction. We determined the MinD-binding site of FtsZ using computational, mutational and biochemical analyses. Our study showed that MinD binds to the H10 helix of FtsZ. Single-point mutations at the charged residues in the H10 helix resulted in a decrease in the FtsZ affinity towards MinD. Based on our findings, we propose a novel model for MinCD-FtsZ interaction, where MinD through its direct interaction with FtsZ would trigger MinC activity to inhibit FtsZ functions.
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921
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Adeniran C, Hamelberg D. Redox-Specific Allosteric Modulation of the Conformational Dynamics of κB DNA by Pirin in the NF-κB Supramolecular Complex. Biochemistry 2017; 56:5002-5010. [DOI: 10.1021/acs.biochem.7b00528] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Charles Adeniran
- Department of Chemistry and the Center for Diagnostics & Therapeutics, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Donald Hamelberg
- Department of Chemistry and the Center for Diagnostics & Therapeutics, Georgia State University, Atlanta, Georgia 30302-3965, United States
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922
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Sierra EM, Pereira MR, Maester TC, Gomes-Pepe ES, Mendoza ER, Lemos EGDM. Halotolerant aminopeptidase M29 from Mesorhizobium SEMIA 3007 with biotechnological potential and its impact on biofilm synthesis. Sci Rep 2017; 7:10684. [PMID: 28878230 PMCID: PMC5587760 DOI: 10.1038/s41598-017-10932-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 08/16/2017] [Indexed: 12/04/2022] Open
Abstract
The aminopeptidase gene from Mesorhizobium SEMIA3007 was cloned and overexpressed in Escherichia coli. The enzyme called MesoAmp exhibited optimum activity at pH 8.5 and 45 °C and was strongly activated by Co2+ and Mn2+. Under these reaction conditions, the enzyme displayed Km and kcat values of 0.2364 ± 0.018 mM and 712.1 ± 88.12 s−1, respectively. Additionally, the enzyme showed remarkable stability in organic solvents and was active at high concentrations of NaCl, suggesting that the enzyme might be suitable for use in biotechnology. MesoAmp is responsible for 40% of the organism’s aminopeptidase activity. However, the enzyme’s absence does not affect bacterial growth in synthetic broth, although it interfered with biofilm synthesis and osmoregulation. To the best of our knowledge, this report describes the first detailed characterization of aminopeptidase from Mesorhizobium and suggests its importance in biofilm formation and osmotic stress tolerance. In summary, this work lays the foundation for potential biotechnological applications and/or the development of environmentally friendly technologies and describes the first solvent- and halo-tolerant aminopeptidases identified from the Mesorhizobium genus and its importance in bacterial metabolism.
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Affiliation(s)
- Elwi Machado Sierra
- Department of Technology, São Paulo State University, Jaboticabal, São Paulo State, Brazil.,Universidad Simón Bolívar, Barranquilla, Colombia
| | | | | | - Elisangela Soares Gomes-Pepe
- Department of Technology, São Paulo State University, Jaboticabal, São Paulo State, Brazil.,Institute for Research in Bioenergy (IPBEN), Jaboticabal, São Paulo State, Brazil
| | - Elkin Rodas Mendoza
- Department of Technology, São Paulo State University, Jaboticabal, São Paulo State, Brazil
| | - Eliana G de Macedo Lemos
- Department of Technology, São Paulo State University, Jaboticabal, São Paulo State, Brazil. .,Institute for Research in Bioenergy (IPBEN), Jaboticabal, São Paulo State, Brazil. .,Av. Prof. Paulo Donato Castellane, s/n. Jaboticabal, Post code 14884-900, São Paulo State, Brazil.
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923
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Meysman P, Titeca K, Eyckerman S, Tavernier J, Goethals B, Martens L, Valkenborg D, Laukens K. Protein complex analysis: From raw protein lists to protein interaction networks. MASS SPECTROMETRY REVIEWS 2017; 36:600-614. [PMID: 26709718 DOI: 10.1002/mas.21485] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Accepted: 11/17/2015] [Indexed: 06/05/2023]
Abstract
The elucidation of molecular interaction networks is one of the pivotal challenges in the study of biology. Affinity purification-mass spectrometry and other co-complex methods have become widely employed experimental techniques to identify protein complexes. These techniques typically suffer from a high number of false negatives and false positive contaminants due to technical shortcomings and purification biases. To support a diverse range of experimental designs and approaches, a large number of computational methods have been proposed to filter, infer and validate protein interaction networks from experimental pull-down MS data. Nevertheless, this expansion of available methods complicates the selection of the most optimal ones to support systems biology-driven knowledge extraction. In this review, we give an overview of the most commonly used computational methods to process and interpret co-complex results, and we discuss the issues and unsolved problems that still exist within the field. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 36:600-614, 2017.
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Affiliation(s)
- Pieter Meysman
- Advanced Database Research and Modelling (ADReM), Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
- Biomedical Informatics Research Center Antwerp (biomina), University of Antwerp/Antwerp University Hospital, Edegem, Belgium
| | - Kevin Titeca
- Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium
- Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Sven Eyckerman
- Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium
- Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Jan Tavernier
- Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium
- Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Bart Goethals
- Advanced Database Research and Modelling (ADReM), Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
| | - Lennart Martens
- Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium
- Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Dirk Valkenborg
- Flemish Institute for Technological Research (VITO), Mol, Belgium
- IBioStat, Hasselt University, Hasselt, Belgium
- CFP-CeProMa, University of Antwerp, Antwerp, Belgium
| | - Kris Laukens
- Advanced Database Research and Modelling (ADReM), Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
- Biomedical Informatics Research Center Antwerp (biomina), University of Antwerp/Antwerp University Hospital, Edegem, Belgium
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924
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Wu Y, Li YH, Li X, Zou Y, Liao HL, Liu L, Chen YG, Bierer D, Hu HG. A novel peptide stapling strategy enables the retention of ring-closing amino acid side chains for the Wnt/β-catenin signalling pathway. Chem Sci 2017; 8:7368-7373. [PMID: 29163887 PMCID: PMC5672839 DOI: 10.1039/c7sc02420g] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 08/29/2017] [Indexed: 12/14/2022] Open
Abstract
An alternative all-hydrocarbon stapling approach in which the amino acid side chains are retained at the stapled positions.
The all-hydrocarbon peptide stapling strategy has recently been extensively explored in drug discovery. There remains the potential for improvement regarding the retention of the amino acid side chains at the stapled positions. Herein, we describe a new series of amino acids that not only contain the native side chains, but also carry the alkenyl arms that are needed for the ring-closing stapling chemistry. We incorporate the new amino acids into a β-catenin-binding domain of Axin (469–482) and develop a new category of stapled peptides with the retention of the native side chains. These stapled peptides exhibit high α-helicity, strong proteolytic stability and good cell permeability. Biochemical experiments demonstrate that these stapled peptides can activate β-catenin more efficiently than canonical stapled peptides due to the presence of extra side chains. We expect that the new side-chain-retention stapling method would expand the scope of the all-hydrocarbon stapled peptide strategy by retaining some important peripheral residues for protein–protein interactions or preserving key hydrophilic side chains to improve solubility.
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Affiliation(s)
- Ye Wu
- School of Pharmacy , Second Military Medical University , Shanghai 200433 , China . .,School of Pharmacy , Chengdu Medical College , Chengdu 610083 , China
| | - Ye-Hua Li
- Tsinghua-Peking Center for Life Sciences , Tsinghua University , Beijing 100084 , China .
| | - Xiang Li
- School of Pharmacy , Second Military Medical University , Shanghai 200433 , China .
| | - Yan Zou
- School of Pharmacy , Second Military Medical University , Shanghai 200433 , China .
| | - Hong-Li Liao
- School of Pharmacy , Chengdu Medical College , Chengdu 610083 , China
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences , Tsinghua University , Beijing 100084 , China .
| | - Ye-Guang Chen
- Tsinghua-Peking Center for Life Sciences , Tsinghua University , Beijing 100084 , China .
| | - Donald Bierer
- Bayer AG , Department of Medicinal Chemistry , Aprather Weg 18A , Wuppertal 42096 , Germany .
| | - Hong-Gang Hu
- School of Pharmacy , Second Military Medical University , Shanghai 200433 , China .
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925
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Lee W, Park EJ, Min G, Choi J, Na DH, Bae JS. Dual Functioned Pegylated Phospholipid Micelles Containing Cationic Antimicrobial Decapeptide for Treating Sepsis. Am J Cancer Res 2017; 7:3759-3767. [PMID: 29109774 PMCID: PMC5667346 DOI: 10.7150/thno.20734] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 07/04/2017] [Indexed: 02/06/2023] Open
Abstract
Despite intensive investigation of molecular mechanisms underlying the pathogenesis of sepsis, many aspects of sepsis remain unresolved; this hampers the development of appropriate therapeutics. In the present study, we developed a biologic nanomedicine containing a cationic antimicrobial decapeptide KSLW (KKVVFWVKFK), self-associated with biocompatible and biodegradable PEGylated phospholipid micelles (PLM), and analyzed its efficacy for treating sepsis. KSLW was modified with polyethylene glycol (PEG)-aldehyde or was conjugated with distearoylphosphatidylethanolamine (DSPE) -PEG-aldehyde. We compared the antibacterial and antiseptic effects of PEG-KSLW and PLM-KSLW with those of unmodified KSLW both in vitro and in vivo. We found that the PLM-KSLW improved the survival rate of sepsis mouse models without undesired immune responses, and inhibited lipopolysaccharide (LPS)-induced severe vascular inflammatory responses in human umbilical vein endothelial cells compared with unmodified KSLW or PEG-KSLW. Furthermore, PLM-KSLW dramatically reduced the bacterial count and inhibited bacterial growth. We also found a new role of PLM-KSLW in tightening vascular barrier integrity by binding to the glycine/tyrosine-rich domain of occludin (OCLN). Our results showed that PLM-KSLW had a more effective antiseptic effect than KSLW or PEG-KSLW, possibly because of its high affinity toward OCLN. Moreover, PLM-KSLW could be potentially used to treat severe vascular inflammatory diseases, including sepsis and septic shock.
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926
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Chakraborti S, Sarkar J, Bhuyan R, Chakraborti T. Role of curcumin in PLD activation by Arf6-cytohesin1 signaling axis in U46619-stimulated pulmonary artery smooth muscle cells. Mol Cell Biochem 2017; 438:97-109. [PMID: 28780751 DOI: 10.1007/s11010-017-3117-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 07/15/2017] [Indexed: 01/01/2023]
Abstract
Phospholipase D (PLD) catalyzes the hydrolysis of phosphatidylcholine to produce phosphatidic acid (PA) which in some cell types play a pivotal role in agonist-induced increase in NADPH oxidase-derived [Formula: see text]production. Involvement of ADP ribosylation factor (Arf) in agonist-induced activation of PLD is known for smooth muscle cells of systemic arteries, but not in pulmonary artery smooth muscle cells (PASMCs). Additionally, role of cytohesin in this scenario is unknown in PASMCs. We, therefore, determined the involvement of Arf and cytohesin in U46619-induced stimulation of PLD in PASMCs, and the probable mechanism by which curcumin, a natural phenolic compound, inhibits the U46619 response. Treatment of PASMCs with U46619 stimulated PLD activity in the cell membrane, which was inhibited upon pretreatment with SQ29548 (Tp receptor antagonist), FIPI (PLD inhibitor), SecinH3 (inhibitor of cytohesins), and curcumin. Transfection of the cells with Tp, Arf-6, and cytohesin-1 siRNA inhibited U46619-induced activation of PLD. Upon treatment of the cells with U46619, Arf-6 and cytohesin-1 were translocated and associated in the cell membrane, which were not inhibited upon pretreatment of the cells with curcumin. Cytohesin-1 appeared to be necessary for in vitro binding of GTPγS with Arf-6; however, addition of curcumin inhibited binding of GTPγS with Arf-6 even in the presence of cytohesin-1. Our computational study suggests that although curcumin to some extent binds with Tp receptor, yet the inhibition of Arf6GDP to Arf6GTP conversion appeared to be an important mechanism by which curcumin inhibits U46619-induced increase in PLD activity in PASMCs.
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Affiliation(s)
- Sajal Chakraborti
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, West Bengal, 741235, India.
| | - Jaganmay Sarkar
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, West Bengal, 741235, India
| | - Rajabrata Bhuyan
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, West Bengal, 741235, India
| | - Tapati Chakraborti
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, West Bengal, 741235, India
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927
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Vinhote JFC, Lima DB, Menezes RRPPBD, Mello CP, de Souza BM, Havt A, Palma MS, Santos RPD, Albuquerque ELD, Freire VN, Martins AMC. Trypanocidal activity of mastoparan from Polybia paulista wasp venom by interaction with TcGAPDH. Toxicon 2017; 137:168-172. [PMID: 28826757 DOI: 10.1016/j.toxicon.2017.08.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 07/31/2017] [Accepted: 08/02/2017] [Indexed: 11/25/2022]
Abstract
Chagas disease, considered a neglected disease, is a parasitic infection caused by Trypanosoma cruzi, which is endemic throughout the world. Previously, the antimicrobial effect of Mastoparan (MP) from Polybia paulista wasp venom against bacteria was described. To continue the study, we report in this short communication the antimicrobial effect of MP against Trypanosoma cruzi. MP inhibits all T. cruzi developmental forms through the inhibition of TcGAPDH suggested by the molecular docking. In conclusion, we suggest there is an antimicrobial effect also on T. cruzi.
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Affiliation(s)
| | - Dânya Bandeira Lima
- Department of Clinical and Toxicological Analyses, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | | | - Clarissa Perdigão Mello
- Department of Clinical and Toxicological Analyses, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | | | - Alexandre Havt
- Department of Physiology and Pharmacology, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Mario Sérgio Palma
- Institute of Biosciences of Rio Claro, São Paulo State University, Brazil
| | | | - Eudenilson Lins de Albuquerque
- Department of Biophysics and Pharmacology, Federal University of Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | | | - Alice Maria Costa Martins
- Department of Clinical and Toxicological Analyses, Federal University of Ceará, Fortaleza, Ceará, Brazil.
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928
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Halakou F, Kilic ES, Cukuroglu E, Keskin O, Gursoy A. Enriching Traditional Protein-protein Interaction Networks with Alternative Conformations of Proteins. Sci Rep 2017; 7:7180. [PMID: 28775330 PMCID: PMC5543104 DOI: 10.1038/s41598-017-07351-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 06/27/2017] [Indexed: 12/19/2022] Open
Abstract
Traditional Protein-Protein Interaction (PPI) networks, which use a node and edge representation, lack some valuable information about the mechanistic details of biological processes. Mapping protein structures to these PPI networks not only provides structural details of each interaction but also helps us to find the mutual exclusive interactions. Yet it is not a comprehensive representation as it neglects the conformational changes of proteins which may lead to different interactions, functions, and downstream signalling. In this study, we proposed a new representation for structural PPI networks inspecting the alternative conformations of proteins. We performed a large-scale study by creating breast cancer metastasis network and equipped it with different conformers of proteins. Our results showed that although 88% of proteins in our network has at least two structures in Protein Data Bank (PDB), only 22% of them have alternative conformations and the remaining proteins have different regions saved in PDB. However, using even this small set of alternative conformations we observed a considerable increase in our protein docking predictions. Our protein-protein interaction predictions increased from 54% to 76% using the alternative conformations. We also showed the benefits of investigating structural data and alternative conformations of proteins through three case studies.
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Affiliation(s)
- Farideh Halakou
- Department of Computer Engineering, Koc University, Istanbul, 34450, Turkey
| | - Emel Sen Kilic
- Department of Chemical and Biological Engineering, Koc University, Istanbul, 34450, Turkey.,Microbiology, Immunology and Cell Biology Department, West Virginia University, Morgantown, 26505, WV, USA
| | - Engin Cukuroglu
- Computational Sciences and Engineering, Graduate School of Sciences and Engineering, Koc University, Istanbul, 34450, Turkey
| | - Ozlem Keskin
- Department of Chemical and Biological Engineering, Koc University, Istanbul, 34450, Turkey
| | - Attila Gursoy
- Department of Computer Engineering, Koc University, Istanbul, 34450, Turkey.
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929
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The Effect of RGD/NGR Peptide Modification of Melanoma Differentiation-Associated Gene-7/Interleukin-24 on Its Receptor Attachment, an In Silico Analysis. Cancer Biother Radiopharm 2017; 32:205-214. [DOI: 10.1089/cbr.2017.2195] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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930
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Rossi M, Spichty M, Attorri L, Distante C, Nervi C, Salvati S, Vitelli L. Eicosapentaenoic acid modulates the synergistic action of CREB1 and ID/E2A family members in the rat pup brain and mouse embryonic stem cells. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2017; 1860:870-884. [PMID: 28666847 DOI: 10.1016/j.bbagrm.2017.06.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 06/01/2017] [Accepted: 06/20/2017] [Indexed: 12/13/2022]
Abstract
The aim of this study was to investigate the molecular mechanism by which eicosapentaenoic acid (EPA) may exert neuroprotective effects through an "EPA-cyclic AMP response element-binding protein (CREB)" signaling pathway. The current study reveals that EPA modulates the exquisite interplay of interaction of CREB1 with the inhibitor of DNA binding (ID) and E2A family members, thereby delivering mechanistic insights into specific neural differentiation program. In this scenario, our work provides evidence for the capability of CREB1 to sequester ID:E2A family members in brain tissues and neural differentiating mouse embryonic stem cells (mESCs) through formation of a [CREB1]2:ID2:E47 tetrameric complex.In essence, the molecular function of CREB1 is to dynamically regulate the location-specific assembly or disassembly of basic-helix-loop-helix (bHLH):HLH protein complexes to mediate the activation of neural/glial target genes. Together, these findings support the one-to-many binding mechanism of CREB1 and indicate that EPA treatment potentiates the integration of CREB dependent signaling with HLH/bHLH transcriptional network, adding specificity to the CREB1-mediated gene regulation during neural/glial differentiation. Our current research on the EPA-CREB axis could reveal new molecular targets for treating neurogenerative disease.
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Affiliation(s)
- Maurizio Rossi
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Martin Spichty
- Laboratory of Biology and Modelling of the Cell, Lyon University, ENS Lyon, University Claude Bernard, CNRS UMR 5239, INSERM U1210, 46 allée d'Italie, Site Jacques Monod, F-69007 Lyon, France
| | - Lucilla Attorri
- Department of Public Veterinary Health and Food Safety, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Chiara Distante
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Clara Nervi
- Department of Medical and Surgical Sciences and Biotechnologies, University of Roma "La Sapienza", Corso della Repubblica 79, 04100, Latina, Italy
| | - Serafina Salvati
- Department of Public Veterinary Health and Food Safety, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Luigi Vitelli
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy.
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931
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Stephen P, Lin SX. RNA-dependent RNA polymerase: Addressing Zika outbreak by a phylogeny-based drug target study. Chem Biol Drug Des 2017. [PMID: 28636772 DOI: 10.1111/cbdd.13054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Since the first major outbreak of Zika virus (ZIKV) in 2007, ZIKV is spreading explosively through South and Central America, and recent reports in highly populated developing countries alarm the possibility of a more catastrophic outbreak. ZIKV infection in pregnant women leads to embryonic microcephaly and Guillain-Barré syndrome in adults. At present, there is limited understanding of the infectious mechanism, and no approved therapy has been reported. Despite the withdrawal of public health emergency, the WHO still considers the ZIKV as a highly significant and long-term public health challenge that the situation has to be addressed rapidly. Non-structural protein 5 is essential for capping and replication of viral RNA and comprises a methyltransferase and RNA-dependent RNA polymerase (RdRp) domain. We used molecular modeling to obtain the structure of ZIKV RdRp, and by molecular docking and phylogeny analysis, we here demonstrate the potential sites for drug screening. Two metal binding sites and an NS3-interacting region in ZIKV RdRp are demonstrated as potential drug screening sites. The docked structures reveal a remarkable degree of conservation at the substrate binding site and the potential drug screening sites. A phylogeny-based approach is provided for an emergency preparedness, where similar class of ligands could target phylogenetically related proteins.
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Affiliation(s)
- Preyesh Stephen
- Laboratory of Molecular Endocrinology, CHU Research Center, Laval University, Québec, Canada
| | - Sheng-Xiang Lin
- Laboratory of Molecular Endocrinology, CHU Research Center, Laval University, Québec, Canada
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932
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Cruciani M, Etna MP, Camilli R, Giacomini E, Percario ZA, Severa M, Sandini S, Rizzo F, Brandi V, Balsamo G, Polticelli F, Affabris E, Pantosti A, Bagnoli F, Coccia EM. Staphylococcus aureus Esx Factors Control Human Dendritic Cell Functions Conditioning Th1/Th17 Response. Front Cell Infect Microbiol 2017; 7:330. [PMID: 28785545 PMCID: PMC5519619 DOI: 10.3389/fcimb.2017.00330] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 07/05/2017] [Indexed: 02/01/2023] Open
Abstract
The opportunistic pathogen Staphylococcus aureus (S. aureus) is a major cause of nosocomial- and community-acquired infections. In addition, many antibiotic-resistant strains are emerging worldwide, thus, there is an urgent unmet need to pinpoint novel therapeutic and prophylactic strategies. In the present study, we characterized the impact of infection with the pandemic methicillin-resistant USA300 S. aureus strain on human primary dendritic cells (DC), key initiators and regulators of immune responses. In particular, among staphylococcal virulence factors, the function of EsxA and EsxB, two small acidic dimeric proteins secreted by the type VII-like secretion system Ess (ESAT-6-like secretion system), was investigated in human DC setting. A comparative analysis of bacterial entry, replication rate as well as DC maturation, apoptosis, signaling pathway activation and cytokine production was performed by using wild type (wt) USA300 and three isogenic mutants carrying the deletion of esxA (ΔesxA), esxB (ΔesxB), or both genes (ΔesxAB). The S. aureus mutant lacking only the EsxA protein (ΔesxA) stimulated a stronger pro-apoptotic phenotype in infected DC as compared to wt USA300, ΔesxAB, and ΔesxB strains. When the mutant carrying the esxB deletion (ΔesxB) was analyzed, a higher production of both regulatory and pro-inflammatory mediators was found in the infected DC with respect to those challenged with the wt counterpart and the other esx mutants. In accordance with these data, supernatant derived from ΔesxB-infected DC promoted a stronger release of both IFN-γ and IL-17 from CD4+ T cells as compared with those conditioned with supernatants derived from wild type USA300-, ΔesxAB-, and ΔesxA-infected cultures. Although, the interaction of S. aureus with human DC is not yet fully understood, our data suggest that both cytokine production and apoptotic process are modulated by Esx factors, thus indicating a possible role of these proteins in the modulation of DC-mediated immunity to S. aureus.
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Affiliation(s)
- Melania Cruciani
- Department of Science, University Roma TreRome, Italy.,Department of Infectious Diseases, Istituto Superiore di SanitàRome, Italy
| | - Marilena P Etna
- Department of Infectious Diseases, Istituto Superiore di SanitàRome, Italy
| | - Romina Camilli
- Department of Infectious Diseases, Istituto Superiore di SanitàRome, Italy
| | - Elena Giacomini
- Department of Infectious Diseases, Istituto Superiore di SanitàRome, Italy
| | | | - Martina Severa
- Department of Infectious Diseases, Istituto Superiore di SanitàRome, Italy
| | - Silvia Sandini
- Department of Infectious Diseases, Istituto Superiore di SanitàRome, Italy
| | - Fabiana Rizzo
- Department of Infectious Diseases, Istituto Superiore di SanitàRome, Italy
| | | | | | - Fabio Polticelli
- Department of Science, University Roma TreRome, Italy.,National Institute of Nuclear Physics, Roma Tre UniversityRome, Italy
| | | | - Annalisa Pantosti
- Department of Infectious Diseases, Istituto Superiore di SanitàRome, Italy
| | | | - Eliana M Coccia
- Department of Infectious Diseases, Istituto Superiore di SanitàRome, Italy
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933
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Akhter Y, Thakur S. Targets of ubiquitin like system in mycobacteria and related actinobacterial species. Microbiol Res 2017; 204:9-29. [PMID: 28870295 DOI: 10.1016/j.micres.2017.07.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 06/22/2017] [Accepted: 07/05/2017] [Indexed: 12/22/2022]
Abstract
Protein turnover and recycling is a prerequisite in all living organisms to maintain normal cellular physiology. Many bacteria are proteasome deficient but they possess typical protease enzymes for carrying out protein turnover. However, several groups of actinobacteria such as mycobacteria harbor both proteasome and proteases. In these bacteria, for cellular protein turnover the target proteins undergo post-translational modification referred as pupylation in which a small protein Pup (prokaryotic ubiquitin-like protein) is tagged to the specific lysine residues of the target proteins and after that those target proteins undergo proteasomal degradation. Thus, Pup serves as a degradation signal, helps in directing proteins toward the bacterial proteasome for a turnover. Although the Pup-proteasome system has a multifaceted role in environmental stresses, pathogenicity and regulation of cellular signaling, but the fate of all types of pupylation such as mono and polypupylation on the proteins is still not completely understood. In this review, we present the mechanisms involved in the activation and conjugation of Pup to the target proteins, describing the structural sketch of pupylation and fundamental differences between the eukaryotic ubiquitin-proteasome and bacterial Pup-proteasome systems. We are also presenting a concise classification and cataloging of the complete battery of experimentally identified Pup-substrates from various species of actinobacteria.
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Affiliation(s)
- Yusuf Akhter
- School of Life Sciences, Central University of Himachal Pradesh, Shahpur, District-Kangra, Himachal Pradesh, 176206, India.
| | - Shweta Thakur
- School of Life Sciences, Central University of Himachal Pradesh, Shahpur, District-Kangra, Himachal Pradesh, 176206, India
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934
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Liu H, Kong X, Chen F. Mkrn3 functions as a novel ubiquitin E3 ligase to inhibit Nptx1 during puberty initiation. Oncotarget 2017; 8:85102-85109. [PMID: 29156706 PMCID: PMC5689596 DOI: 10.18632/oncotarget.19347] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 06/26/2017] [Indexed: 12/12/2022] Open
Abstract
Central precocious puberty (CPP) is attributed to the disorder of some trigger factors those can activate the hypothalamic-pituitary-gonadal axis controlled by GnRH neurons. Many recent studies reveal one of those trigger factors, Makorin ring finger protein 3 (Mkrn3), whose loss-of-function mutations are implicated in CPP. Although Mkrn3 contained zinc Ring finger domain is considered as a putative E3 ubiquitin ligase, its actual function is never reported. Here, our results demonstrated that in mice hypothalamus before and when puberty initiated, Mkrn3 expressed the reversed tendency with Nptx1, which is an important secreted protein for neuron development. Furthermore, our data manifested that Mkrn3 interacted and suppressed Nptx1 activity. And the Ring finger domain of Mkrn3 contained was determined to be essential for binding with Nptx1 for its polyubiquitination during the puberty initiation. Our study shed light on the molecular insights into the function of Mkrn3 in the events of puberty initiation.
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Affiliation(s)
- Huifang Liu
- Department of Endocrinology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiangxin Kong
- Department of Endocrinology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Fengling Chen
- Department of Endocrinology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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935
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Currie SL, Doane JJ, Evans KS, Bhachech N, Madison BJ, Lau DKW, McIntosh LP, Skalicky JJ, Clark KA, Graves BJ. ETV4 and AP1 Transcription Factors Form Multivalent Interactions with three Sites on the MED25 Activator-Interacting Domain. J Mol Biol 2017; 429:2975-2995. [PMID: 28728983 DOI: 10.1016/j.jmb.2017.06.024] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 06/04/2017] [Accepted: 06/05/2017] [Indexed: 01/05/2023]
Abstract
The recruitment of transcriptional cofactors by sequence-specific transcription factors challenges the basis of high affinity and selective interactions. Extending previous studies that the N-terminal activation domain (AD) of ETV5 interacts with Mediator subunit 25 (MED25), we establish that similar, aromatic-rich motifs located both in the AD and in the DNA-binding domain (DBD) of the related ETS factor ETV4 interact with MED25. These ETV4 regions bind MED25 independently, display distinct kinetics, and combine to contribute to a high-affinity interaction of full-length ETV4 with MED25. High-affinity interactions with MED25 are specific for the ETV1/4/5 subfamily as other ETS factors display weaker binding. The AD binds to a single site on MED25 and the DBD interacts with three MED25 sites, allowing for simultaneous binding of both domains in full-length ETV4. MED25 also stimulates the in vitro DNA binding activity of ETV4 by relieving autoinhibition. ETV1/4/5 factors are often overexpressed in prostate cancer and genome-wide studies in a prostate cancer cell line indicate that ETV4 and MED25 occupy enhancers that are enriched for ETS-binding sequences and are both functionally important for the transcription of genes regulated by these enhancers. AP1-motifs, which bind JUN and FOS transcription factor families, were observed in MED25-occupied regions and JUN/FOS also contact MED25; FOS strongly binds to the same MED25 site as ETV4 AD and JUN interacts with the other two MED25 sites. In summary, we describe features of the multivalent ETV4- and AP1-MED25 interactions, thereby implicating these factors in the recruitment of MED25 to transcriptional control elements.
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Affiliation(s)
- Simon L Currie
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT, 84112-5500, USA; Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, 84112-5500, USA
| | - Jedediah J Doane
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT, 84112-5500, USA; Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, 84112-5500, USA
| | - Kathryn S Evans
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT, 84112-5500, USA; Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, 84112-5500, USA
| | - Niraja Bhachech
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT, 84112-5500, USA; Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, 84112-5500, USA
| | - Bethany J Madison
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT, 84112-5500, USA; Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, 84112-5500, USA
| | - Desmond K W Lau
- Departments of Biochemistry and Molecular Biology, Department of Chemistry, and Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Lawrence P McIntosh
- Departments of Biochemistry and Molecular Biology, Department of Chemistry, and Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Jack J Skalicky
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, 84112-5650, USA
| | - Kathleen A Clark
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT, 84112-5500, USA; Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, 84112-5500, USA
| | - Barbara J Graves
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT, 84112-5500, USA; Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, 84112-5500, USA; Howard Hughes Medical Institute, Chevy Chase, MD, 20815-6789, USA.
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936
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Involvement of FANCD2 in Energy Metabolism via ATP5α. Sci Rep 2017; 7:4921. [PMID: 28687786 PMCID: PMC5501830 DOI: 10.1038/s41598-017-05150-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 05/24/2017] [Indexed: 12/31/2022] Open
Abstract
Growing evidence supports a general hypothesis that aging and cancer are diseases related to energy metabolism. However, the involvement of Fanconi Anemia (FA) signaling, a unique genetic model system for studying human aging or cancer, in energy metabolism remains elusive. Here, we report that FA complementation group D2 protein (FANCD2) functionally impacts mitochondrial ATP production through its interaction with ATP5α, whereas this relationship was not observed in the mutant FANCD2 (K561R)-carrying cells. Moreover, while ATP5α is present within the mitochondria in wild-type cells, it is instead located mostly outside in cells that carry the non-monoubiquitinated FANCD2. In addition, mitochondrial ATP production is significantly reduced in these cells, compared to those cells carrying wtFANCD2. We identified one region (AA42-72) of ATP5α, contributing to the interaction between ATP5α and FANCD2, which was confirmed by protein docking analysis. Further, we demonstrated that mtATP5α (∆AA42-72) showed an aberrant localization, and resulted in a decreased ATP production, similar to what was observed in non-monoubiquitinated FANCD2-carrying cells. Collectively, our study demonstrates a novel role of FANCD2 in governing cellular ATP production, and advances our understanding of how defective FA signaling contributes to aging and cancer at the energy metabolism level.
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937
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Bhattacharjee S, Dasgupta R, Bagchi A. Elucidation of the molecular mechanism of heat shock proteins and its correlation with K722Q mutations in Lon protease. Biosystems 2017; 159:12-22. [PMID: 28676239 DOI: 10.1016/j.biosystems.2017.06.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 04/22/2017] [Accepted: 06/22/2017] [Indexed: 10/19/2022]
Abstract
Cells withstand the effects of temperature change with the help of small heat shock proteins IbpA and IbpB. The IbpAB protein complex interacts with Lon protease in their free form and gets degraded at physiological temperature when there is no temperature stress. However, the proteolytic degradation of IbpAB is diminished when Lon is mutated. The mutation K722Q in Lon brings about some structural changes so that the proteolytic interactions between the heat shock proteins with that of the mutated Lon protease are lost. However, the detailed molecular aspects of the interactions are not yet fully understood. In the present, we made an attempt to analyze the biochemical aspects of the interactions between the small heat shock proteins IbpAB with wild type and mutant Lon protease. We for the first time deciphered the molecular details of the mechanism of interaction of small heat shock proteins with Lon protease bearing K722Q mutation i.e. the interaction pattern of heat shock proteins with mutant Lon protease at physiological temperature in absence of proteolytic machinery. Our study may therefore be useful to elucidate the mechanistic details of the correlation with IbpA, IbpB and Lon protease.
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Affiliation(s)
- Sanchari Bhattacharjee
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, Nadia, India.
| | - Rakhi Dasgupta
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, Nadia, India.
| | - Angshuman Bagchi
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, Nadia, India.
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938
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Verma P, Patel GK, Kar B, Sharma AK. A case of neofunctionalization of a Putranjiva roxburghii PNP protein to trypsin inhibitor by disruption of PNP-UDP domain through an insert containing inhibitory site. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 260:19-30. [PMID: 28554472 DOI: 10.1016/j.plantsci.2017.03.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 03/11/2017] [Accepted: 03/25/2017] [Indexed: 05/24/2023]
Abstract
The attainment of new function by a protein is achieved through convergent/divergent evolution. In present work, the sequence analysis of a 34kDa protein from Putranjiva roxburghii, earlier reported as a potent trypsin inhibitor, showed resemblance to some of the wound inducible and vegetative storage proteins. A detailed sequence analysis revealed that these proteins belong to PNP-UDP family. In case of P. roxburghii protein, an approximately 46 residue insert disrupts the PNP domain. Similar disruption of PNP domain is observed in related plant proteins. The characterization of recombinant full length and truncated (without 46 residue insert) forms of P. roxburghii PNP family protein (PRpnp) unraveled that trypsin inhibitory active site is located within the insert. The truncated form containing uninterrupted PNP domain showed strong PNP enzymatic activity where it hydrolyzed the N-glycosidic bond of inosine and guanosine. The full length protein, however, showed weak PNP enzyme activity which may be due to presence of the insert. These results indicate towards the neofunctionalization of PRpnp to a potent trypsin inhibitor through an insert containing inhibitory residue to cater to the needs of plant defense. The similar wound inducible and vegetative storage proteins may have also evolved due to evolutionary needs.
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Affiliation(s)
- Preeti Verma
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247 667, India
| | - Girijesh K Patel
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247 667, India
| | - Bibekananda Kar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247 667, India
| | - Ashwani K Sharma
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247 667, India.
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939
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Režen T, Ogris I, Sever M, Merzel F, Golic Grdadolnik S, Rozman D. Evaluation of Selected CYP51A1 Polymorphisms in View of Interactions with Substrate and Redox Partner. Front Pharmacol 2017; 8:417. [PMID: 28713270 PMCID: PMC5492350 DOI: 10.3389/fphar.2017.00417] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Accepted: 06/13/2017] [Indexed: 01/16/2023] Open
Abstract
Cholesterol is essential for development, growth, and maintenance of organisms. Mutations in cholesterol biosynthetic genes are embryonic lethal and few polymorphisms have been so far associated with pathologies in humans. Previous analyses show that lanosterol 14α-demethylase (CYP51A1) from the late part of cholesterol biosynthesis has only a few missense mutations with low minor allele frequencies and low association with pathologies in humans. The aim of this study is to evaluate the role of amino acid changes in the natural missense mutations of the hCYP51A1 protein. We searched SNP databases for existing polymorphisms of CYP51A1 and evaluated their effect on protein function. We found rare variants causing detrimental missense mutations of CYP51A1. Some missense variants were also associated with a phenotype in humans. Two missense variants have been prepared for testing enzymatic activity in vitro but failed to produce a P450 spectrum. We performed molecular modeling of three selected missense variants to evaluate the effect of the amino acid substitution on potential interaction with its substrate and the obligatory redox partner POR. We show that two of the variants, R277L and especially D152G, have possibly lower binding potential toward obligatory redox partner POR. D152G and R431H have also potentially lower affinity toward the substrate lanosterol. We evaluated the potential effect of damaging variants also using data from other in vitro CYP51A1 mutants. In conclusion, we propose to include damaging CYP51A1 variants into personalized diagnostics to improve genetic counseling for certain rare disease phenotypes.
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Affiliation(s)
- Tadeja Režen
- Faculty of Medicine, Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry, University of LjubljanaLjubljana, Slovenia
| | - Iza Ogris
- Faculty of Medicine, Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry, University of LjubljanaLjubljana, Slovenia
| | - Marko Sever
- Department of Biomolecular Structure, National Institute of ChemistryLjubljana, Slovenia
| | - Franci Merzel
- Department of Biomolecular Structure, National Institute of ChemistryLjubljana, Slovenia
| | | | - Damjana Rozman
- Faculty of Medicine, Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry, University of LjubljanaLjubljana, Slovenia
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940
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Fukui K, Iino H, Baba S, Kumasaka T, Kuramitsu S, Yano T. Crystal structure and DNA-binding property of the ATPase domain of bacterial mismatch repair endonuclease MutL from Aquifex aeolicus. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1178-1187. [PMID: 28668638 DOI: 10.1016/j.bbapap.2017.06.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 06/23/2017] [Accepted: 06/27/2017] [Indexed: 01/06/2023]
Abstract
DNA mismatch repair (MMR) system corrects mismatched bases that are generated mainly by DNA replication errors. The repair system excises the error-containing single-stranded region and enables the re-synthesis of the strand. In the early reactions of MMR, MutL endonuclease incises the newly-synthesized/error-containing strand of the duplex to initiate the downstream excision reaction. MutL endonuclease consists of the N-terminal ATPase and C-terminal endonuclease domains. In this study, we report the crystal structure of the ATPase domain of MutL endonuclease from Aquifex aeolicus. The overall structure of the domain was similar to those of human MutL homologs and Escherichia coli MutL, although E. coli MutL has no endonuclease activity. The ATPase domain was comprised of two subdomains: the N-terminal ATP-binding subdomain and the C-terminal α-β sandwich subdomain. Site-directed mutagenesis experiment identified DNA-interacting eight basic amino acid residues, which were distributed across both the two subdomains and formed a DNA-binding cleft. Docking simulation between the structures of the ATPase and endonuclease domains generated a reliable model structure for the full-length A. aeolicus MutL, which satisfies our previous result of small-angle X-ray scattering analysis. On the basis of the model structure and further experimental results, we concluded that the two separate DNA-binding sites in the full-length A. aeolicus MutL simultaneously bind a dsDNA molecule.
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Affiliation(s)
- Kenji Fukui
- Department of Biochemistry, Osaka Medical College, 2-7 Daigakumachi, Takatsuki, Osaka 569-8686, Japan.
| | - Hitoshi Iino
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo-cho, Sayo-Gun, Hyogo 679-5148, Japan
| | - Seiki Baba
- Japan Synchrotron Radiation Research Institute (JASRI), SPring-8, Kouto, Sayo, Hyogo 679-5198, Japan
| | - Takashi Kumasaka
- Japan Synchrotron Radiation Research Institute (JASRI), SPring-8, Kouto, Sayo, Hyogo 679-5198, Japan
| | - Seiki Kuramitsu
- Department of Biological Sciences, Osaka University, 1-1 Machikaneyamacho, Toyonaka, Osaka 560-0043, Japan
| | - Takato Yano
- Department of Biochemistry, Osaka Medical College, 2-7 Daigakumachi, Takatsuki, Osaka 569-8686, Japan.
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941
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Sun S, Lei Y, Li Q, Wu Y, Zhang L, Mu PP, Ji GQ, Tang CX, Wang YQ, Gao J, Gao J, Li L, Zhuo L, Li YQ, Gao DS. Neuropilin-1 is a glial cell line-derived neurotrophic factor receptor in glioblastoma. Oncotarget 2017; 8:74019-74035. [PMID: 29088765 PMCID: PMC5650320 DOI: 10.18632/oncotarget.18630] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 05/12/2017] [Indexed: 01/13/2023] Open
Abstract
The aim of this study was to identify the receptor for glial cell line-derived neurotrophic factor (GDNF) in glioblastoma multiforme (GBM). After GST pull-down assays, membrane proteins purified from C6 rat glioma cells were subjected to liquid chromatography-tandem mass spectrometry (LC-MS/MS). The differentially expressed proteins were annotated using Gene Ontology, and neuropilin-1 (NRP1) was identified as the putative GDNF receptor in glioma. NRP1 was more highly expressed in human GBM brains and C6 rat glioma cells than in normal human brains or primary rat astrocytes. Immunofluorescence staining showed that NRP1 was recruited to the membrane by GDNF, and NRP1 co-immunoprecipitated with GDNF. Using the NRP1 and GDNF protein structures to assess molecular docking in the ZDOCK server and visualization with the PyMOL Molecular Graphics System revealed 8 H-bonds and stable positive and negative electrostatic interactions between NRP1 and GDNF. RNAi knockdown of NRP1 reduced proliferation of C6 glioma cells when stimulated with GDNF. NRP1 was an independent risk factor for both survival and recurrence in GBM patients. High NRP1 mRNA expression correlated with shorter OS and DFS (OS: χ2=4.6720, P=0.0307; DFS: χ2=11.013, P=0.0009). NRP1 is thus a GDNF receptor in glioma cells and a potential therapeutic target.
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Affiliation(s)
- Shen Sun
- Department of Anatomy and Histology, The Fourth Military Medical University, Xi'an, Shanxi, China.,Department of Neurobiology and Anatomy, Xuzhou Key Laboratory of Neurobiology, Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu, China.,Department of Histology and Embryology, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yu Lei
- Department of Neurobiology and Anatomy, Xuzhou Key Laboratory of Neurobiology, Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu, China.,Department of Neurobiology, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
| | - Qi Li
- Department of Neurobiology and Anatomy, Xuzhou Key Laboratory of Neurobiology, Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yue Wu
- Department of Neurobiology and Anatomy, Xuzhou Key Laboratory of Neurobiology, Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Lin Zhang
- Department of Neurobiology and Anatomy, Xuzhou Key Laboratory of Neurobiology, Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Pei-Pei Mu
- Department of Neurobiology and Anatomy, Xuzhou Key Laboratory of Neurobiology, Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Guang-Quan Ji
- Department of Neurobiology and Anatomy, Xuzhou Key Laboratory of Neurobiology, Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Chuan-Xi Tang
- Department of Neurobiology and Anatomy, Xuzhou Key Laboratory of Neurobiology, Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yu-Qian Wang
- Department of Neurobiology and Anatomy, Xuzhou Key Laboratory of Neurobiology, Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Jian Gao
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Jin Gao
- Department of Neurobiology and Anatomy, Xuzhou Key Laboratory of Neurobiology, Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Li Li
- Department of Pathophysiology, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Lang Zhuo
- Department of Epidemiology, School of Public Health, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yun-Qing Li
- Department of Anatomy and Histology, The Fourth Military Medical University, Xi'an, Shanxi, China
| | - Dian-Shuai Gao
- Department of Anatomy and Histology, The Fourth Military Medical University, Xi'an, Shanxi, China.,Department of Neurobiology and Anatomy, Xuzhou Key Laboratory of Neurobiology, Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu, China
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942
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Sugino H, Usui T, Shimada T, Nakano M, Ogasawara H, Ishihama A, Hirata A. A structural sketch of RcdA, a transcription factor controlling the master regulator of biofilm formation. FEBS Lett 2017; 591:2019-2031. [PMID: 28608551 DOI: 10.1002/1873-3468.12713] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 05/30/2017] [Accepted: 06/01/2017] [Indexed: 12/23/2022]
Abstract
RcdA is a regulator of curlin subunit gene D, the master regulator of biofilm formation in Escherichia coli. Here, we determined the X-ray structure of RcdA at 2.55 Å resolution. RcdA consists of an N-terminal DNA-binding domain (DBD) containing a helix-turn-helix (HTH) motif and a C-terminal dimerization domain, and forms a homodimer in crystals. A computational docking model of the RcdA-DNA complex allowed prediction of the candidate residues responsible for DNA binding. Our structure-guided mutagenesis, in combination with gel shift assay, atomic force microscopic observation, and reporter assay, indicate that R32 in α2 of the HTH motif plays an essential role in the recognition and binding of target DNA while T46 in α3 influences the mode of oligomerization. These results provide insights into the DNA-binding mode of RcdA.
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Affiliation(s)
- Hirotaka Sugino
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Matsuyama, Japan
| | - Takanori Usui
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Matsuyama, Japan
| | - Tomohiro Shimada
- School of Agriculture, Meiji University, Tama-ku, Kawasaki-shi, Kanagawa, Japan
| | - Masahiro Nakano
- Department of Virus Research, Institute for Frontier Life and Medical Science, Kyoto University, Japan
| | - Hiroshi Ogasawara
- Research Center for Supports to Advanced Science, Division of Gene Research, Shinshu University, Ueda, Nagano, Japan.,Research Center for Fungal and Microbial Dynamism, Shinshu University, Nagano, Japan
| | - Akira Ishihama
- Micro-Nano Technology Research Center and Department of Frontier Bioscience, Hosei University, Koganei, Tokyo, Japan
| | - Akira Hirata
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Matsuyama, Japan
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943
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Computational modeling of protein assemblies. Curr Opin Struct Biol 2017; 44:179-189. [DOI: 10.1016/j.sbi.2017.04.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 04/07/2017] [Accepted: 04/11/2017] [Indexed: 01/18/2023]
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944
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Immuno-informatics based approaches to identify CD8+ T cell epitopes within the Leishmania donovani 3-ectonucleotidase in cured visceral leishmaniasis subjects. Microbes Infect 2017; 19:358-369. [DOI: 10.1016/j.micinf.2017.03.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Revised: 03/10/2017] [Accepted: 03/24/2017] [Indexed: 01/22/2023]
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945
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Alagarasu K, Patil PS, Shil P, Seervi M, Kakade MB, Tillu H, Salunke A. In-vitro effect of human cathelicidin antimicrobial peptide LL-37 on dengue virus type 2. Peptides 2017; 92:23-30. [PMID: 28400226 DOI: 10.1016/j.peptides.2017.04.002] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 03/30/2017] [Accepted: 04/07/2017] [Indexed: 12/17/2022]
Abstract
Human Cathelicidin antimicrobial peptide LL-37 is known to have antiviral activity against many viruses. In the present study, we investigated the in-vitro effect of LL-37 on dengue virus type 2 (DENV-2) infection and replication in Vero E6 cells. To study the effect of pretreatment of virus or cells with LL-37, the virus was pretreated with different concentrations of LL-37 (2.5μM-15μM) or scrambled (Scr) LL-37(5μM-15μM) and used for infection or the cells were first treated with LL-37 and infected. To study the effect of LL-37 post infection (PI), the cells were infected first followed by addition of LL-37 to the culture medium 24h after infection. In all conditions, after the incubation, the culture supernatant was assessed for viral RNA copy number by real time RT-PCR, infectious virus particles by focus forming unit assay (FFU) and non structural protein 1 (NS1) antigen levels by ELISA. Percentage of infection was assessed using immunoflourescence assay (IFA). The results revealed that pretreatment of virus with 10-15μM LL-37 significantly reduced its infectivity as compared to virus control (P<0.0001). Moreover, pretreatment of virus with 10-15μM LL-37 significantly reduced the levels of viral genomic RNA and NS1 antigen (P<0.0001). Treatment of virus with 10-15μM LL-37 resulted in two to three log reduction of mean log10 FFU/ml as compared to virus control (P<0.0001). Treatment of the virus with scrambled LL-37 had no effect on percentage of infection and viral load as compared to virus control cultures (P>0.05). Pretreatment of cells before infection or addition of LL-37 to the culture 24h PI had no effect on viral load. Molecular docking studies revealed possible binding of LL-37 to both the units of DENV envelope (E) protein dimer. Together, the in-vitro experiments and in-silico analyses suggest that LL-37 inhibits DENV-2 at the stage of entry into the cells by binding to the E protein. The results might have implications for prophylaxis against DENV infections and need further in-vivo studies.
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Affiliation(s)
- K Alagarasu
- Dengue/Chikungunya Group, ICMR-National Institute of Virology, 20A, Dr. Ambedkar Road, Pune 411001, Maharashtra, India.
| | - P S Patil
- Dengue/Chikungunya Group, ICMR-National Institute of Virology, 20A, Dr. Ambedkar Road, Pune 411001, Maharashtra, India
| | - P Shil
- Bioinformatics Group, Microbial Containment Complex, ICMR-National Institute of Virology, Sus Road, Pashan, Pune 411021, Maharashtra, India
| | - M Seervi
- Dengue/Chikungunya Group, ICMR-National Institute of Virology, 20A, Dr. Ambedkar Road, Pune 411001, Maharashtra, India
| | - M B Kakade
- Dengue/Chikungunya Group, ICMR-National Institute of Virology, 20A, Dr. Ambedkar Road, Pune 411001, Maharashtra, India
| | - H Tillu
- Dengue/Chikungunya Group, ICMR-National Institute of Virology, 20A, Dr. Ambedkar Road, Pune 411001, Maharashtra, India
| | - A Salunke
- Dengue/Chikungunya Group, ICMR-National Institute of Virology, 20A, Dr. Ambedkar Road, Pune 411001, Maharashtra, India
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946
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Moktan H, Zhou DH. Wing 1 of protein HOP2 is as important as helix 3 in DNA binding by MD simulation. J Biomol Struct Dyn 2017; 36:1853-1866. [PMID: 28531371 DOI: 10.1080/07391102.2017.1333458] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The repair of programmed DNA double-strand breaks through recombination is required for proper association and disjunction of the meiotic homologous chromosomes. Meiosis-specific protein HOP2 plays essential roles in recombination by promoting recombinase activities. The N-terminal domain of HOP2 interacts with DNA through helix 3 (H3) and wing 1 (W1). Mutations in wing 1 (Y65A/K67A/Q68A) slightly weakened the binding but mutations in helices 2 and 3 (Q30A/K44A/K49A) nearly abolished the binding. To better understand such differential effects at atomic level, molecular dynamics simulations were employed. Despite losing some hydrogen bonds, the W1-mutant DNA complex was rescued by stronger hydrophobic interactions. For the wild type and W1-mutant, the protein was found to slide along the DNA grooves as the DNA rolls along its double-helix axis. This motion could be functionally important to facilitate the precise positioning of the single-stranded DNA with the homologous double-stranded DNA. The sliding motion was reduced in the W1-mutant. The H-mutant nearly lost all intermolecular interactions. Moreover, an additional mutation in wing 1 (Y65A/K67A/Q68A/K69A) also caused complete complex dissociation. Therefore, both wing 1 and helix 3 make important contribution to the DNA binding, which could be important to the strand invasion function of HOP2 homodimer and HOP2-MND1 heterodimer. Similar to cocking a medieval crossbow with the archer's foot placed in the stirrup, wing 1 may push the minor groove to cause distortion while helix 3 grabs the major groove.
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Affiliation(s)
- Hem Moktan
- a Department of Physics , Oklahoma State University , Stillwater , OK , USA
| | - Donghua H Zhou
- a Department of Physics , Oklahoma State University , Stillwater , OK , USA
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947
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Molecular characterization of Netrin-1 and APP receptor binding: New leads to block the progression of senile plaques in Alzheimer's disease. Biochem Biophys Res Commun 2017; 488:466-470. [PMID: 28501620 DOI: 10.1016/j.bbrc.2017.05.056] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 05/09/2017] [Indexed: 01/20/2023]
Abstract
Alzheimer's disease is a growing concern in the context of the increasing lifespan of the populations. The work presented here is part of the fight against this threat. It supports a therapeutic approach to reduce the incidence of Alzheimer's disease, taking advantage of the specific binding of several domains of Netrin-1 to the β-amyloid precursor protein. This basic knowledge shall then be used to predict, design or characterize lead compounds that may in turn inhibit/delay Alzheimer's disease's progression, extending the therapeutic offer of the other leads already being investigated in this line. The present work is focused on the interaction of the various portions of APP with the three domains of Netrin-1, the so-called LamNT, EGF-like and NTR domains respectively. It reveals in detail which portions of APP and Netrin-1 are specifically involved in these interactions, using ELISA technique in combination with protein-protein binding simulations. So far unsuspected interaction sites located in Netrin-1 EGF-like and NTR domains open possibilities for new therapeutic approaches in which these sites will be specifically targeted.
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948
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Iqbal A, Goldfeder MB, Marques-Porto R, Asif H, Souza JGD, Faria F, Chudzinski-Tavassi AM. Revisiting antithrombotic therapeutics; sculptin, a novel specific, competitive, reversible, scissile and tight binding inhibitor of thrombin. Sci Rep 2017; 7:1431. [PMID: 28469161 PMCID: PMC5431157 DOI: 10.1038/s41598-017-01486-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 03/30/2017] [Indexed: 02/01/2023] Open
Abstract
Thrombin is a multifunctional enzyme with a key role in the coagulation cascade. Its functional modulation can culminate into normal blood coagulation or thrombosis. Thus, the identification of novel potent inhibitors of thrombin are of immense importance. Sculptin is the first specific thrombin inhibitor identified in the transcriptomics analysis of tick’s salivary glands. It consists of 168 residues having four similar repeats and evolutionary diverged from hirudin. Sculptin is a competitive, specific and reversible inhibitor of thrombin with a Ki of 18.3 ± 1.9 pM (kon 4.04 ± 0.03 × 107 M−1 s−1 and koff 0.65 ± 0.04 × 10−3 s−1). It is slowly consumed by thrombin eventually losing its activity. Contrary, sculptin is hydrolyzed by factor Xa and each polypeptide fragment is able to inhibit thrombin independently. A single domain of sculptin alone retains ~45% of inhibitory activity, which could bind thrombin in a bivalent fashion. The formation of a small turn/helical-like structure by active site binding residues of sculptin might have made it a more potent thrombin inhibitor. In addition, sculptin prolongs global coagulation parameters. In conclusion, sculptin and its independent domain(s) have strong potential to become novel antithrombotic therapeutics.
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Affiliation(s)
- Asif Iqbal
- Laboratory of Biochemistry and Biophysics, Butantan Institute, Sao Paulo, SP, Brazil.,Centre of Excellence in New Target Discovery (CENTD), Butantan Institute, São Paulo, SP, Brazil
| | - Mauricio Barbugiani Goldfeder
- Laboratory of Biochemistry and Biophysics, Butantan Institute, Sao Paulo, SP, Brazil.,Centre of Excellence in New Target Discovery (CENTD), Butantan Institute, São Paulo, SP, Brazil
| | - Rafael Marques-Porto
- Laboratory of Biochemistry and Biophysics, Butantan Institute, Sao Paulo, SP, Brazil
| | - Huma Asif
- Laboratory of Gene Expression in Eukaryotes, Butantan Institute, São Paulo, SP, Brazil
| | - Jean Gabriel de Souza
- Laboratory of Biochemistry and Biophysics, Butantan Institute, Sao Paulo, SP, Brazil.,Centre of Excellence in New Target Discovery (CENTD), Butantan Institute, São Paulo, SP, Brazil
| | - Fernanda Faria
- Laboratory of Biochemistry and Biophysics, Butantan Institute, Sao Paulo, SP, Brazil.,Centre of Excellence in New Target Discovery (CENTD), Butantan Institute, São Paulo, SP, Brazil
| | - Ana Marisa Chudzinski-Tavassi
- Laboratory of Biochemistry and Biophysics, Butantan Institute, Sao Paulo, SP, Brazil. .,Centre of Excellence in New Target Discovery (CENTD), Butantan Institute, São Paulo, SP, Brazil.
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949
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Nicholas DA, Zhang K, Hung C, Glasgow S, Aruni AW, Unternaehrer J, Payne KJ, Langridge WHR, De Leon M. Palmitic acid is a toll-like receptor 4 ligand that induces human dendritic cell secretion of IL-1β. PLoS One 2017; 12:e0176793. [PMID: 28463985 PMCID: PMC5413048 DOI: 10.1371/journal.pone.0176793] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 04/17/2017] [Indexed: 01/22/2023] Open
Abstract
Palmitic acid (PA) and other saturated fatty acids are known to stimulate pro-inflammatory responses in human immune cells via Toll-like receptor 4 (TLR4). However, the molecular mechanism responsible for fatty acid stimulation of TLR4 remains unknown. Here, we demonstrate that PA functions as a ligand for TLR4 on human monocyte derived dendritic cells (MoDCs). Hydrophobicity protein modeling indicated PA can associate with the hydrophobic binding pocket of TLR4 adaptor protein MD-2. Isothermal titration calorimetry quantified heat absorption that occurred during PA titration into TLR4/MD2, indicating that PA binds to TLR4/MD2. Treatment of human MoDCs with PA resulted in endocytosis of TLR4, further supporting the function of PA as a TLR4 agonist. In addition, PA stimulated DC maturation and activation based on the upregulation of DC costimulatory factors CD86 and CD83. Further experiments showed that PA induced TLR4 dependent secretion of the pro-inflammatory cytokine IL-1β. Lastly, our experimental data show that PA stimulation of NF-κB canonical pathway activation is regulated by TLR4 signaling and that reactive oxygen species may be important in upregulating this pro-inflammatory response. Our experiments demonstrate for the first time that PA activation of TLR4 occurs in response to direct molecular interactions between PA and MD-2. In summary, our findings suggest a likely molecular mechanism for PA induction of pro-inflammatory immune responses in human dendritic cells expressing TLR4.
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Affiliation(s)
- Dequina A. Nicholas
- Center for Health Disparities and Molecular Medicine, Loma Linda University School of Medicine, Loma Linda, California, United States of America
- Division of Biochemistry, Department of Basic Sciences, Loma Linda University School Medicine, Loma Linda, California, United States of America
| | - Kangling Zhang
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Christopher Hung
- Center for Health Disparities and Molecular Medicine, Loma Linda University School of Medicine, Loma Linda, California, United States of America
- Division of Biochemistry, Department of Basic Sciences, Loma Linda University School Medicine, Loma Linda, California, United States of America
| | - Shane Glasgow
- Center for Health Disparities and Molecular Medicine, Loma Linda University School of Medicine, Loma Linda, California, United States of America
- Division of Biochemistry, Department of Basic Sciences, Loma Linda University School Medicine, Loma Linda, California, United States of America
| | - Aruni Wilson Aruni
- Department of Basic Sciences, Division of Microbiology and Molecular Genetics, Loma Linda University School Medicine, Loma Linda, California, United States of America
| | - Juli Unternaehrer
- Center for Health Disparities and Molecular Medicine, Loma Linda University School of Medicine, Loma Linda, California, United States of America
- Division of Biochemistry, Department of Basic Sciences, Loma Linda University School Medicine, Loma Linda, California, United States of America
| | - Kimberly J. Payne
- Center for Health Disparities and Molecular Medicine, Loma Linda University School of Medicine, Loma Linda, California, United States of America
- Department of Anatomy and Physiology, Loma Linda University School Medicine, Loma Linda, California, United States of America
| | - William H. R. Langridge
- Center for Health Disparities and Molecular Medicine, Loma Linda University School of Medicine, Loma Linda, California, United States of America
- Division of Biochemistry, Department of Basic Sciences, Loma Linda University School Medicine, Loma Linda, California, United States of America
| | - Marino De Leon
- Center for Health Disparities and Molecular Medicine, Loma Linda University School of Medicine, Loma Linda, California, United States of America
- Department of Basic Sciences, Division of Physiology, Loma Linda University School Medicine, Loma Linda, California, United States of America
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950
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Seo T, Sakon T, Nakazawa S, Nishioka A, Watanabe K, Matsumoto K, Akasaka M, Shioi N, Sawada H, Araki S. Haemorrhagic snake venom metalloproteases and human
ADAM
s cleave
LRP
5/6, which disrupts cell–cell adhesions
in vitro
and induces haemorrhage
in vivo. FEBS J 2017; 284:1657-1671. [DOI: 10.1111/febs.14066] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 03/11/2017] [Accepted: 03/22/2017] [Indexed: 11/25/2022]
Affiliation(s)
- Tadahiko Seo
- Sugashima Marine Biological Laboratory Graduate School of Science Nagoya University Japan
| | - Taketo Sakon
- Sugashima Marine Biological Laboratory Graduate School of Science Nagoya University Japan
| | - Shiori Nakazawa
- Sugashima Marine Biological Laboratory Graduate School of Science Nagoya University Japan
| | - Asuka Nishioka
- Sugashima Marine Biological Laboratory Graduate School of Science Nagoya University Japan
| | - Kohei Watanabe
- Sugashima Marine Biological Laboratory Graduate School of Science Nagoya University Japan
| | - Kaori Matsumoto
- Sugashima Marine Biological Laboratory Graduate School of Science Nagoya University Japan
| | - Mari Akasaka
- Sugashima Marine Biological Laboratory Graduate School of Science Nagoya University Japan
| | - Narumi Shioi
- Department of Chemistry Faculty of Science Fukuoka University Japan
| | - Hitoshi Sawada
- Sugashima Marine Biological Laboratory Graduate School of Science Nagoya University Japan
| | - Satohiko Araki
- Sugashima Marine Biological Laboratory Graduate School of Science Nagoya University Japan
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