1001
|
Keskin O, Tuncbag N, Gursoy A. Predicting Protein–Protein Interactions from the Molecular to the Proteome Level. Chem Rev 2016; 116:4884-909. [DOI: 10.1021/acs.chemrev.5b00683] [Citation(s) in RCA: 207] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
| | - Nurcan Tuncbag
- Graduate
School of Informatics, Department of Health Informatics, Middle East Technical University, 06800 Ankara, Turkey
| | | |
Collapse
|
1002
|
Zhu L, Peigneur S, Gao B, Zhang S, Tytgat J, Zhu S. Target-Driven Positive Selection at Hot Spots of Scorpion Toxins Uncovers Their Potential in Design of Insecticides. Mol Biol Evol 2016; 33:1907-20. [PMID: 27189560 DOI: 10.1093/molbev/msw065] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Positive selection sites (PSSs), a class of amino acid sites with an excess of nonsynonymous to synonymous substitutions, are indicators of adaptive molecular evolution and have been detected in many protein families involved in a diversity of biological processes by statistical approaches. However, few studies are conducted to evaluate their functional significance and the driving force behind the evolution (i.e., agent of selection). Scorpion α-toxins are a class of multigene family of peptide neurotoxins affecting voltage-gated Na(+ )(Nav) channels, whose members exhibit differential potency and preference for insect and mammalian Nav channels. In this study, we undertook a systematical molecular dissection of nearly all the PSSs newly characterized in the Mesobuthus α-toxin family and a two-residue insertion ((19)AlaPhe(20)) located within a positively selected loop via mutational analysis of α-like MeuNaTxα-5, one member affecting both insect and mammalian Nav channels. This allows to identify hot-spot residues on its functional face involved in interaction with the receptor site of Nav channels, which comprises two PSSs (Ile(40) and Leu(41)) and the small insertion, both located on two spatially separated functional loops. Mutations at these hot-spots resulted in a remarkably decreased anti-mammalian activity in MeuNaTxα-5 with partially impaired or enhanced insecticide activity, suggesting the potential of PSSs in designing promising candidate insecticides from scorpion α-like toxins. Based on an experiment-guided toxin-channel complex model and high evolutionary variability in the receptor site of predators and prey of scorpions, we provide new evidence for target-driven adaptive evolution of scorpion toxins to deal with their targets' diversity.
Collapse
Affiliation(s)
- Limei Zhu
- Group of Peptide Biology and Evolution, State Key Laboratory of Integrated Management of Pest Insects & Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Steve Peigneur
- Laboratory of Toxicology, University of Leuven, Leuven, Belgium
| | - Bin Gao
- Group of Peptide Biology and Evolution, State Key Laboratory of Integrated Management of Pest Insects & Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Shangfei Zhang
- Group of Peptide Biology and Evolution, State Key Laboratory of Integrated Management of Pest Insects & Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jan Tytgat
- Laboratory of Toxicology, University of Leuven, Leuven, Belgium
| | - Shunyi Zhu
- Group of Peptide Biology and Evolution, State Key Laboratory of Integrated Management of Pest Insects & Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
1003
|
Meza-Romero R, Benedek G, Leng L, Bucala R, Vandenbark AA. Predicted structure of MIF/CD74 and RTL1000/CD74 complexes. Metab Brain Dis 2016; 31:249-55. [PMID: 26851955 PMCID: PMC5248574 DOI: 10.1007/s11011-016-9798-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 01/19/2016] [Indexed: 01/03/2023]
Abstract
Macrophage migration inhibitory factor (MIF) is a key cytokine in autoimmune and inflammatory diseases that attracts and then retains activated immune cells from the periphery to the tissues. MIF exists as a homotrimer and its effects are mediated through its primary receptor, CD74 (the class II invariant chain that exhibits a highly structured trimerization domain), present on class II expressing cells. Although a number of binding residues have been identified between MIF and CD74 trimers, their spatial orientation has not been established. Using a docking program in silico, we have modeled binding interactions between CD74 and MIF as well as CD74 and a competitive MIF inhibitor, RTL1000, a partial MHC class II construct that is currently in clinical trials for multiple sclerosis. These analyses revealed 3 binding sites on the MIF trimer that each were predicted to bind one CD74 trimer through interactions with two distinct 5 amino acid determinants. Surprisingly, predicted binding of one CD74 trimer to a single RTL1000 antagonist utilized the same two 5 residue determinants, providing strong suggestive evidence in support of the MIF binding regions on CD74. Taken together, our structural modeling predicts a new MIF(CD74)3 dodecamer that may provide the basis for increased MIF potency and the requirement for ~3-fold excess RTL1000 to achieve full antagonism.
Collapse
Affiliation(s)
- Roberto Meza-Romero
- Neuroimmunology Research, VA Portland Health Care System, 3710 SW US Veterans Hosp. Rd, Portland, OR, 97239, USA
- Tykeson MS Research Laboratory, Department of Neurology UHS-46, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd, Portland, OR, USA
| | - Gil Benedek
- Neuroimmunology Research, VA Portland Health Care System, 3710 SW US Veterans Hosp. Rd, Portland, OR, 97239, USA
- Tykeson MS Research Laboratory, Department of Neurology UHS-46, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd, Portland, OR, USA
| | - Lin Leng
- Department of Internal Medicine Yale University School of Medicine, 330 Cedar St, New Haven, CT, 06520, USA
| | - Richard Bucala
- Department of Internal Medicine Yale University School of Medicine, 330 Cedar St, New Haven, CT, 06520, USA
| | - Arthur A Vandenbark
- Neuroimmunology Research, VA Portland Health Care System, 3710 SW US Veterans Hosp. Rd, Portland, OR, 97239, USA.
- Tykeson MS Research Laboratory, Department of Neurology UHS-46, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd, Portland, OR, USA.
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd, Portland, OR, USA.
| |
Collapse
|
1004
|
Novoseletsky VN, Volyntseva AD, Shaitan KV, Kirpichnikov MP, Feofanov AV. Modeling of the Binding of Peptide Blockers to Voltage-Gated Potassium Channels: Approaches and Evidence. Acta Naturae 2016; 8:35-46. [PMID: 27437138 PMCID: PMC4947987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Indexed: 11/13/2022] Open
Abstract
Modeling of the structure of voltage-gated potassium (KV) channels bound to peptide blockers aims to identify the key amino acid residues dictating affinity and provide insights into the toxin-channel interface. Computational approaches open up possibilities for in silico rational design of selective blockers, new molecular tools to study the cellular distribution and functional roles of potassium channels. It is anticipated that optimized blockers will advance the development of drugs that reduce over activation of potassium channels and attenuate the associated malfunction. Starting with an overview of the recent advances in computational simulation strategies to predict the bound state orientations of peptide pore blockers relative to KV-channels, we go on to review algorithms for the analysis of intermolecular interactions, and then take a look at the results of their application.
Collapse
Affiliation(s)
- V. N. Novoseletsky
- M.V.Lomonosov Moscow State University, Faculty of Biology, Leninskie Gory 1, bldg. 12, 119992 , Moscow, Russia
| | - A. D. Volyntseva
- M.V.Lomonosov Moscow State University, Faculty of Biology, Leninskie Gory 1, bldg. 12, 119992 , Moscow, Russia
| | - K. V. Shaitan
- M.V.Lomonosov Moscow State University, Faculty of Biology, Leninskie Gory 1, bldg. 12, 119992 , Moscow, Russia
| | - M. P. Kirpichnikov
- M.V.Lomonosov Moscow State University, Faculty of Biology, Leninskie Gory 1, bldg. 12, 119992 , Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho- Maklaya str. 16/10, 117997, Moscow, Russia
| | - A. V. Feofanov
- M.V.Lomonosov Moscow State University, Faculty of Biology, Leninskie Gory 1, bldg. 12, 119992 , Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho- Maklaya str. 16/10, 117997, Moscow, Russia
| |
Collapse
|
1005
|
Hui WQ, Cheng Q, Liu TY, Ouyang Q. Homology modeling, docking, and molecular dynamics simulation of the receptor GALR2 and its interactions with galanin and a positive allosteric modulator. J Mol Model 2016; 22:90. [PMID: 27021209 DOI: 10.1007/s00894-016-2944-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 02/22/2016] [Indexed: 12/17/2022]
Abstract
Galanin receptor type 2 (GALR2) is a class A G-protein-coupled receptor (GPCR), and it has been reported that orthosteric ligands and positive allosteric modulators (PAMs) of GALR2 could potentially be used to treat epilepsy. So far, the X-ray structure of this receptor has not been resolved, and knowledge of the 3D structure of GALR2 may prove informative in attempts to design novel ligands and to explore the mechanism for the allosteric modulation of this receptor. In this study, homology modeling was used to obtain several GALR2 models using known templates. ProSA-web Z-scores and Ramachandran plots as well as pre-screening against a test dataset of known compounds were all utilized to select the best model of GALR2. Molecular dockings of galanin (a peptide) and a nonpeptide ligand were carried out to choose the (GALR2 model)-galanin complex that showed the closest agreement with the corresponding experimental data. Finally, a 50-ns MD simulation was performed to study the interactions between the GALR2 model and the synthetic and endogenous ligands. The results from docking and MD simulation showed that, besides the reported residues, Tyr160(4.60), Ile105(3.32), Ala274(7.35), and Tyr163(ECL2) also appear to play important roles in the binding of galanin. The potential allosteric binding pockets in the GALR2 model were then investigated via MD simulation. The results indicated that the mechanism for the allosteric modulation caused by PAMs is the binding of the PAM at pocket III, which is formed by galanin, ECL2, TM2, TM3, and ECL1; this results in the disruption of the Na(+)-binding site and/or the Na(+) ion pathway, leading to GALR2 agonism.
Collapse
Affiliation(s)
- Wen-Qi Hui
- College of Pharmacy, Third Military Medical University, No. 30 Gaotanyan Street, Chongqing, 400038, China
| | - Qi Cheng
- College of Pharmacy, Third Military Medical University, No. 30 Gaotanyan Street, Chongqing, 400038, China
| | - Tian-Yu Liu
- College of Pharmacy, Third Military Medical University, No. 30 Gaotanyan Street, Chongqing, 400038, China.
| | - Qin Ouyang
- College of Pharmacy, Third Military Medical University, No. 30 Gaotanyan Street, Chongqing, 400038, China.
| |
Collapse
|
1006
|
Shao W, Zhu W, Wang Y, Lu J, Jin G, Wang Y, Su W. Rational design and molecular engineering of peptide aptamers to target human pancreatic trypsin in acute pancreatitis. BIOTECHNOL BIOPROC E 2016. [DOI: 10.1007/s12257-015-0638-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
|
1007
|
Ramírez-Aportela E, López-Blanco JR, Chacón P. FRODOCK 2.0: fast protein–protein docking server. Bioinformatics 2016; 32:2386-8. [DOI: 10.1093/bioinformatics/btw141] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 03/09/2016] [Indexed: 01/09/2023] Open
Abstract
Abstract
Summary: The prediction of protein–protein complexes from the structures of unbound components is a challenging and powerful strategy to decipher the mechanism of many essential biological processes. We present a user-friendly protein–protein docking server based on an improved version of FRODOCK that includes a complementary knowledge-based potential. The web interface provides a very effective tool to explore and select protein–protein models and interactively screen them against experimental distance constraints. The competitive success rates and efficiency achieved allow the retrieval of reliable potential protein–protein binding conformations that can be further refined with more computationally demanding strategies.
Availability and Implementation: The server is free and open to all users with no login requirement at http://frodock.chaconlab.org
Contact: pablo@chaconlab.org
Supplementary information: Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Erney Ramírez-Aportela
- Department of Biological Chemical Physics, Rocasolano Physical Chemistry Institute C.S.I.C, Madrid 28006, Spain
- Centro de Investigaciones Biológicas, CSIC, Madrid E-28040, Spain
| | - José Ramón López-Blanco
- Department of Biological Chemical Physics, Rocasolano Physical Chemistry Institute C.S.I.C, Madrid 28006, Spain
| | - Pablo Chacón
- Department of Biological Chemical Physics, Rocasolano Physical Chemistry Institute C.S.I.C, Madrid 28006, Spain
| |
Collapse
|
1008
|
Kostantin E, Hardy S, Valinsky WC, Kompatscher A, de Baaij JHF, Zolotarov Y, Landry M, Uetani N, Martínez-Cruz LA, Hoenderop JGJ, Shrier A, Tremblay ML. Inhibition of PRL-2·CNNM3 Protein Complex Formation Decreases Breast Cancer Proliferation and Tumor Growth. J Biol Chem 2016; 291:10716-25. [PMID: 26969161 PMCID: PMC4865918 DOI: 10.1074/jbc.m115.705863] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Indexed: 11/06/2022] Open
Abstract
The oncogenic phosphatase of regenerating liver 2 (PRL-2) has been shown to regulate intracellular magnesium levels by forming a complex through an extended amino acid loop present in the Bateman module of the CNNM3 magnesium transporter. Here we identified highly conserved residues located on this amino acid loop critical for the binding with PRL-2. A single point mutation (D426A) of one of those critical amino acids was found to completely disrupt PRL-2·human Cyclin M 3 (CNNM3) complex formation. Whole-cell voltage clamping revealed that expression of CNNM3 influenced the surface current, whereas overexpression of the binding mutant had no effect, indicating that the binding of PRL-2 to CNNM3 is important for the activity of the complex. Interestingly, overexpression of the CNNM3 D426A-binding mutant in cancer cells decreased their ability to proliferate under magnesium-deprived situations and under anchorage-independent growth conditions, demonstrating a PRL-2·CNNM3 complex-dependent oncogenic advantage in a more stringent environment. We further confirmed the importance of this complex in vivo using an orthotopic xenograft breast cancer model. Finally, because molecular modeling showed that the Asp-426 side chain in CNNM3 buries into the catalytic cavity of PRL-2, we showed that a PRL inhibitor could abrogate complex formation, resulting in a decrease in proliferation of human breast cancer cells. In summary, we provide evidence that this fundamental regulatory aspect of PRL-2 in cancer cells could potentially lead to broadly applicable and innovative therapeutic avenues.
Collapse
Affiliation(s)
- Elie Kostantin
- From the Rosalind and Morris Goodman Cancer Research Centre, Montréal, Québec H3A 1A3, Canada, the Departments of Biochemistry and
| | - Serge Hardy
- From the Rosalind and Morris Goodman Cancer Research Centre, Montréal, Québec H3A 1A3, Canada
| | | | - Andreas Kompatscher
- the Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands, and
| | - Jeroen H F de Baaij
- the Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands, and
| | - Yevgen Zolotarov
- From the Rosalind and Morris Goodman Cancer Research Centre, Montréal, Québec H3A 1A3, Canada, the Departments of Biochemistry and
| | - Melissa Landry
- From the Rosalind and Morris Goodman Cancer Research Centre, Montréal, Québec H3A 1A3, Canada
| | - Noriko Uetani
- From the Rosalind and Morris Goodman Cancer Research Centre, Montréal, Québec H3A 1A3, Canada
| | - Luis Alfonso Martínez-Cruz
- the Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Technology Park of Bizkaia, 48160 Derio, Bizkaia, Spain
| | - Joost G J Hoenderop
- the Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands, and
| | - Alvin Shrier
- Physiology, McGill University, Montréal, Québec H3A 0G4, Canada
| | - Michel L Tremblay
- From the Rosalind and Morris Goodman Cancer Research Centre, Montréal, Québec H3A 1A3, Canada, the Departments of Biochemistry and
| |
Collapse
|
1009
|
Key role of Dkk3 protein in inhibition of cancer cell proliferation: An in silico identification. J Theor Biol 2016; 393:98-104. [DOI: 10.1016/j.jtbi.2015.12.029] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 11/09/2015] [Accepted: 12/30/2015] [Indexed: 12/22/2022]
|
1010
|
Nakano CM, Moen E, Byun HS, Ma H, Newman B, McDowell A, Wei T, El-Naggar MY. iBET: Immersive visualization of biological electron-transfer dynamics. J Mol Graph Model 2016; 65:94-9. [PMID: 26955008 DOI: 10.1016/j.jmgm.2016.02.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 01/13/2016] [Accepted: 02/21/2016] [Indexed: 11/30/2022]
Abstract
Recently, we presented a computational framework named VizBET to simulate and visualize biological electron-transfer (ET) dynamics. The visualization process was encapsulated as a plugin to the Visual Molecular Dynamics (VMD) software. However, the user's ability to understand complex, multidimensional ET pathways was severely limited when visualized in 2D on traditional computer monitors. To provide a more accurate representation with enhanced depth perception, we here present an extension of VizBET named iBET to render the VMD model of ET dynamics in a commodity virtual reality (VR) platform. The paper describes detailed procedures to export VMD models into the Unity game engine and render it in an Oculus Rift head mounted display. With the increasing availability of low-cost VR systems like the Rift and rich programmability of game engines, the iBET framework provides a powerful means to explore and understand not only biological ET processes but also a unique experiential tool for broad scientific communities.
Collapse
Affiliation(s)
| | - Erick Moen
- Department of Electrical Engineering, University of Southern California, Los Angeles, CA 90089-0241, USA
| | - Hye Suk Byun
- Department of Physics & Astronomy, University of Southern California, Los Angeles, CA 90089-0484, USA
| | - Heng Ma
- Department of Chemical Engineering, Lamar University, Beaumont, TX 77710, USA
| | - Bradley Newman
- School of Cinematic Arts, University of Southern California, Los Angeles, CA 90089-2211, USA
| | - Alexander McDowell
- School of Cinematic Arts, University of Southern California, Los Angeles, CA 90089-2211, USA
| | - Tao Wei
- Department of Chemical Engineering, Lamar University, Beaumont, TX 77710, USA.
| | - Mohamed Y El-Naggar
- Department of Physics & Astronomy, University of Southern California, Los Angeles, CA 90089-0484, USA; Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089-0371, USA; Department of Chemistry, University of Southern California, Los Angeles, CA 90089-1062, USA.
| |
Collapse
|
1011
|
Kanjanaworakul P, Sawatdichaikul O, Poompuang S. cDNA sequence and protein bioinformatics analyses of MSTN in African catfish (Clarias gariepinus). Mol Biol Rep 2016; 43:283-93. [PMID: 26912268 DOI: 10.1007/s11033-016-3961-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 02/18/2016] [Indexed: 11/28/2022]
Abstract
Myostatin, also known as growth differentiation factor 8, has been identified as a potent negative regulator of skeletal muscle growth. The purpose of this study was to characterize and predict function of the myostatin gene of the African catfish (Cg-MSTN). Expression of Cg-MSTN was determined at three growth stages to establish the relationship between the levels of MSTN transcript and skeletal muscle growth. The partial cDNA sequence of Cg-MSTN was cloned by using published information from its congener walking catfish (Cm-MSTN). The Cg-MSTN was 1194 bp in length encoding a protein of 397 amino acids. The deduced MSTN sequence exhibited key functional sites similar to those of other members of the TGF-β superfamily, especially, the proteolytic processing site (RXXR motif) and nine conserved cysteines at the C-terminal. Expression of MSTN appeared to be correlated with muscle development and growth of African catfish. Protein bioinformatics revealed that the primary sequence of Cg-MSTN shared 98 % sequence identity with that of walking catfish Cm-MSTN with only two different residues, [Formula: see text]. and [Formula: see text]. The proposed model of Cg-MSTN revealed the key point mutation [Formula: see text] causing a 7.35 Å shorter distance between the N- and C-lobes and an approximately 11° narrow angle than those of Cm-MSTN. The substitution of a proline residue near the proteolytic processing site which altered the structure of myostatin may play a critical role in reducing proteolytic activity of this protein in African catfish.
Collapse
Affiliation(s)
- Poonmanee Kanjanaworakul
- Center for Agricultural Biotechnology, Kasetsart University, Nakorn Pathom, 73140, Thailand
- Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE), Bangkok, 10900, Thailand
| | - Orathai Sawatdichaikul
- Department of Nutrition and Health, Institute of Food Research and Product Development, Kasetsart University, Bangkok, 10900, Thailand.
| | - Supawadee Poompuang
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Bangkok, 10900, Thailand.
| |
Collapse
|
1012
|
A potential therapeutic peptide-based neutralizer that potently inhibits Shiga toxin 2 in vitro and in vivo. Sci Rep 2016; 6:21837. [PMID: 26903273 PMCID: PMC4763182 DOI: 10.1038/srep21837] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 01/25/2016] [Indexed: 11/08/2022] Open
Abstract
Shiga toxin 2 (Stx2) is a major virulence factor in infections with Stx-producing Escherichia coli (STEC), which can cause serious clinical complications in humans, such as hemolytic uremic syndrome (HUS). Recently, we screened and identified two peptide-based Stx2 neutralizers, TF-1 and WA-8, which specifically and directly bind to Stx2. Computer simulations suggested that the majority of TF-1 or WA-8 binds tightly at the receptor-binding site 3 of Stx2. The two peptides also effectively inhibited the cytotoxic activity of Stx2 by blocking the binding of Stx2 to target cells. TF-1 exhibits remarkable therapeutic potency in both mice and rat toxicity models. In mice toxicity models, TF-1 provided full protection when mice were injected with 5 LD50 of Stx2. In rat toxicity models, TF-1 reduced fatal tissue damage and completely protected rats from the lethal challenges of Stx2. In these rats, TF-1 significantly decreased the concentration of Stx2 in blood and diminished tissue distribution levels of Stx2. Furthermore, TF-1 effectively protected rats from the pathological effects caused by Stx2, especially in the kidney, thymus, adrenal gland, and lung. Taken together, these results indicate that TF-1 is a promising therapeutic agent against the pathogenicity of Stx2.
Collapse
|
1013
|
Shim JY, Khurana L, Kendall DA. Computational analysis of the CB1 carboxyl-terminus in the receptor-G protein complex. Proteins 2016; 84:532-43. [PMID: 26994549 DOI: 10.1002/prot.24999] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 01/07/2016] [Accepted: 01/19/2016] [Indexed: 01/03/2023]
Abstract
Despite the important role of the carboxyl-terminus (Ct) of the activated brain cannabinoid receptor one (CB1) in the regulation of G protein signaling, a structural understanding of interactions with G proteins is lacking. This is largely due to the highly flexible nature of the CB1 Ct that dynamically adapts its conformation to the presence of G proteins. In the present study, we explored how the CB1 Ct can interact with the G protein by building on our prior modeling of the CB1-Gi complex (Shim, Ahn, and Kendall, The Journal of Biological Chemistry 2013;288:32449-32465) to incorporate a complete CB1 Ct (Glu416(Ct)-Leu472(Ct)). Based on the structural constraints from NMR studies, we employed ROSETTA to predict tertiary folds, ZDOCK to predict docking orientation, and molecular dynamics (MD) simulations to obtain two distinct plausible models of CB1 Ct in the CB1-Gi complex. The resulting models were consistent with the NMR-determined helical structure (H9) in the middle region of the CB1 Ct. The CB1 Ct directly interacted with both Gα and Gβ and stabilized the receptor at the Gi interface. The results of site-directed mutagenesis studies of Glu416(Ct), Asp423(Ct), Asp428(Ct), and Arg444(Ct) of CB1 Ct suggested that the CB1 Ct can influence receptor-G protein coupling by stabilizing the receptor at the Gi interface. This research provided, for the first time, models of the CB1 Ct in contact with the G protein.
Collapse
Affiliation(s)
- Joong-Youn Shim
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina, 27514
| | - Leepakshi Khurana
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut, 06269-3092
| | - Debra A Kendall
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut, 06269-3092
| |
Collapse
|
1014
|
Oliviero G, Stornaiuolo M, D'Atri V, Nici F, Yousif AM, D'Errico S, Piccialli G, Mayol L, Novellino E, Marinelli L, Grieco P, Carotenuto A, Noppen S, Liekens S, Balzarini J, Borbone N. Screening Platform toward New Anti-HIV Aptamers Set on Molecular Docking and Fluorescence Quenching Techniques. Anal Chem 2016; 88:2327-34. [PMID: 26810800 DOI: 10.1021/acs.analchem.5b04268] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
By using a new rapid screening platform set on molecular docking simulations and fluorescence quenching techniques, three new anti-HIV aptamers targeting the viral surface glycoprotein 120 (gp120) were selected, synthesized, and assayed. The use of the short synthetic fluorescent peptide V35-Fluo mimicking the V3 loop of gp120, as the molecular target for fluorescence-quenching binding affinity studies, allowed one to measure the binding affinities of the new aptamers for the HIV-1 gp120 without the need to obtain and purify the full recombinant gp120 protein. The almost perfect correspondence between the calculated Kd and the experimental EC50 on HIV-infected cells confirmed the reliability of the platform as an alternative to the existing methods for aptamer selection and measuring of aptamer-protein equilibria.
Collapse
Affiliation(s)
- Giorgia Oliviero
- University of Naples Federico II , Department of Pharmacy, Napoli, 80131, Italy
| | - Mariano Stornaiuolo
- University of Naples Federico II , Department of Pharmacy, Napoli, 80131, Italy
| | - Valentina D'Atri
- University of Bordeaux , IECB, ARNA laboratory, Pessac, 33600, France.,INSERM , U869, ARNA laboratory, Bordeaux, 33000, France
| | - Fabrizia Nici
- University of Naples Federico II , Department of Pharmacy, Napoli, 80131, Italy
| | - Ali Munaim Yousif
- University of Naples Federico II , Department of Pharmacy, Napoli, 80131, Italy
| | - Stefano D'Errico
- University of Naples Federico II , Department of Pharmacy, Napoli, 80131, Italy
| | - Gennaro Piccialli
- University of Naples Federico II , Department of Pharmacy, Napoli, 80131, Italy.,CNR , Institute of Protein Biochemistry, Napoli, 80131, Italy
| | - Luciano Mayol
- University of Naples Federico II , Department of Pharmacy, Napoli, 80131, Italy
| | - Ettore Novellino
- University of Naples Federico II , Department of Pharmacy, Napoli, 80131, Italy
| | - Luciana Marinelli
- University of Naples Federico II , Department of Pharmacy, Napoli, 80131, Italy
| | - Paolo Grieco
- University of Naples Federico II , Department of Pharmacy, Napoli, 80131, Italy
| | - Alfonso Carotenuto
- University of Naples Federico II , Department of Pharmacy, Napoli, 80131, Italy
| | - Sam Noppen
- KU Leuven , Rega Institute for Medical Research, Leuven, 3000, Belgium
| | - Sandra Liekens
- KU Leuven , Rega Institute for Medical Research, Leuven, 3000, Belgium
| | - Jan Balzarini
- KU Leuven , Rega Institute for Medical Research, Leuven, 3000, Belgium
| | - Nicola Borbone
- University of Naples Federico II , Department of Pharmacy, Napoli, 80131, Italy
| |
Collapse
|
1015
|
Groitl B, Horowitz S, Makepeace KAT, Petrotchenko EV, Borchers CH, Reichmann D, Bardwell JCA, Jakob U. Protein unfolding as a switch from self-recognition to high-affinity client binding. Nat Commun 2016; 7:10357. [PMID: 26787517 PMCID: PMC4735815 DOI: 10.1038/ncomms10357] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 12/02/2015] [Indexed: 01/20/2023] Open
Abstract
Stress-specific activation of the chaperone Hsp33 requires the unfolding of a central linker region. This activation mechanism suggests an intriguing functional relationship between the chaperone's own partial unfolding and its ability to bind other partially folded client proteins. However, identifying where Hsp33 binds its clients has remained a major gap in our understanding of Hsp33's working mechanism. By using site-specific Fluorine-19 nuclear magnetic resonance experiments guided by in vivo crosslinking studies, we now reveal that the partial unfolding of Hsp33's linker region facilitates client binding to an amphipathic docking surface on Hsp33. Furthermore, our results provide experimental evidence for the direct involvement of conditionally disordered regions in unfolded protein binding. The observed structural similarities between Hsp33's own metastable linker region and client proteins present a possible model for how Hsp33 uses protein unfolding as a switch from self-recognition to high-affinity client binding. Under stress conditions the molecular chaperone Hsp33 is activated to process unfolded proteins. Here, the authors use in vivo and in vitro crosslinking and 19F-NMR to elucidate the binding site for misfolded proteins and are able to propose a model for its mechanism of action.
Collapse
Affiliation(s)
- Bastian Groitl
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 830 N-University Avenue, Ann Arbor, Michigan 48109-1048, USA
| | - Scott Horowitz
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 830 N-University Avenue, Ann Arbor, Michigan 48109-1048, USA.,Howard Hughes Medical Institute, University of Michigan, 830 N-University Avenue, Ann Arbor, Michigan 48109-1048, USA
| | - Karl A T Makepeace
- Department of Biochemistry and Microbiology, Genome BC Proteomics Centre, University of Victoria, 4464 Markham Street #3101, Victoria, British Columbia, Canada V8Z5N3
| | - Evgeniy V Petrotchenko
- Department of Biochemistry and Microbiology, Genome BC Proteomics Centre, University of Victoria, 4464 Markham Street #3101, Victoria, British Columbia, Canada V8Z5N3
| | - Christoph H Borchers
- Department of Biochemistry and Microbiology, Genome BC Proteomics Centre, University of Victoria, 4464 Markham Street #3101, Victoria, British Columbia, Canada V8Z5N3
| | - Dana Reichmann
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 830 N-University Avenue, Ann Arbor, Michigan 48109-1048, USA
| | - James C A Bardwell
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 830 N-University Avenue, Ann Arbor, Michigan 48109-1048, USA.,Howard Hughes Medical Institute, University of Michigan, 830 N-University Avenue, Ann Arbor, Michigan 48109-1048, USA
| | - Ursula Jakob
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 830 N-University Avenue, Ann Arbor, Michigan 48109-1048, USA
| |
Collapse
|
1016
|
Kyriakou PK, Ekblad B, Kristiansen PE, Kaznessis YN. Interactions of a class IIb bacteriocin with a model lipid bilayer, investigated through molecular dynamics simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:824-35. [PMID: 26774214 DOI: 10.1016/j.bbamem.2016.01.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 01/06/2016] [Accepted: 01/12/2016] [Indexed: 01/15/2023]
Abstract
The emergence of antibiotic resistant microorganisms poses an alarming threat to global health. Antimicrobial peptides (AMPs) are considered a possible effective alternative to conventional antibiotic therapies. An understanding of the mechanism of action of AMPs is needed in order to better control and optimize their bactericidal activity. Plantaricin EF is a heterodimeric AMP, consisting of two peptides Plantaricin E (PlnE) and Plantaricin F (PlnF). We studied the behavior of these peptides on the surface of a model lipid bilayer. We identified the residues that facilitate peptide-peptide interactions. We also identified residues that mediate interactions of the dimer with the membrane. PlnE interacts with the membrane through amino acids at both its termini, while only the N terminus of PlnF approaches the membrane. By comparing the activity of single-site mutants of the two-peptide bacteriocin and the simulations of the bacteriocin on the surface of a model lipid bilayer, structure activity relationships are proposed. These studies allow us to generate hypotheses that relate biophysical interactions observed in simulations with the experimentally measured activity. We find that single-site amino acid substitutions result in markedly stronger antimicrobial activity when they strengthen the interactions between the two peptides, while, concomitantly, they weaken peptide-membrane association. This effect is more pronounced in the case of the PlnE mutant (G20A), which interacts the strongest with PlnF and the weakest with the membrane while displaying the highest activity.
Collapse
Affiliation(s)
- Panagiota K Kyriakou
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, United States
| | - Bie Ekblad
- Department of Biosciences, University of Oslo, Post box 1041 Blindern, 0316 Oslo, Norway
| | - Per Eugen Kristiansen
- Department of Biosciences, University of Oslo, Post box 1041 Blindern, 0316 Oslo, Norway
| | - Yiannis N Kaznessis
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, United States.
| |
Collapse
|
1017
|
Ahnert SE, Marsh JA, Hernández H, Robinson CV, Teichmann SA. Principles of assembly reveal a periodic table of protein complexes. Science 2016; 350:aaa2245. [PMID: 26659058 DOI: 10.1126/science.aaa2245] [Citation(s) in RCA: 153] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Structural insights into protein complexes have had a broad impact on our understanding of biological function and evolution. In this work, we sought a comprehensive understanding of the general principles underlying quaternary structure organization in protein complexes. We first examined the fundamental steps by which protein complexes can assemble, using experimental and structure-based characterization of assembly pathways. Most assembly transitions can be classified into three basic types, which can then be used to exhaustively enumerate a large set of possible quaternary structure topologies. These topologies, which include the vast majority of observed protein complex structures, enable a natural organization of protein complexes into a periodic table. On the basis of this table, we can accurately predict the expected frequencies of quaternary structure topologies, including those not yet observed. These results have important implications for quaternary structure prediction, modeling, and engineering.
Collapse
Affiliation(s)
- Sebastian E Ahnert
- Theory of Condensed Matter Group, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK
| | - Joseph A Marsh
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK. European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Helena Hernández
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Sarah A Teichmann
- Theory of Condensed Matter Group, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK. European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
| |
Collapse
|
1018
|
Xia L, Xian Y, Wang D, Chen Y, Huang X, Bi X, Yu H, Fu Z, Liu X, Li S, An Z, Luo W, Zhao Q, Xia N. A human monoclonal antibody against HPV16 recognizes an immunodominant and neutralizing epitope partially overlapping with that of H16.V5. Sci Rep 2016; 6:19042. [PMID: 26750243 PMCID: PMC4707464 DOI: 10.1038/srep19042] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 12/03/2015] [Indexed: 11/13/2022] Open
Abstract
The presence of neutralizing epitopes in human papillomavirus (HPV) L1 virus-like particles (VLPs) is the structural basis of prophylactic vaccines. An anti-HPV16 neutralizing monoclonal antibody (N-mAb) 26D1 was isolated from a memory B cell of a human vaccinee. The pre-binding of heparan sulfate to VLPs inhibited the binding of both N-mAbs to the antigen, indicating that the epitopes are critical for viral cell attachment/entry. Hybrid VLP binding with surface loop swapping between types indicated the essential roles of the DE and FG loops for both 26D1 (DEa in particular) and H16.V5 binding. Specifically, Tyr(135) and Val(141) on the DEa loop were shown to be critical residues for 26D1 binding via site-directed mutagenesis. Partially overlap between the epitopes between 26D1 and H16.V5 was shown using pairwise epitope mapping, and their binding difference is demonstrated to be predominantly in DE loop region. In addition, 26D1 epitope is immunodominant epitope recognized by both antibodies elicited by the authentic virus from infected individuals and polyclonal antibodies from vaccinees. Overall, a partially overlapping but distinct neutralizing epitope from that of H16.V5 was identified using a human N-mAb, shedding lights to the antibody arrays as part of human immune response to vaccination and infection.
Collapse
Affiliation(s)
- Lin Xia
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Science, Xiamen University; Xiamen 361105, China
| | - Yangfei Xian
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Science, Xiamen University; Xiamen 361105, China
| | - Daning Wang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Science, Xiamen University; Xiamen 361105, China
| | - Yuanzhi Chen
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Science, Xiamen University; Xiamen 361105, China
| | - Xiaofen Huang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Science, Xiamen University; Xiamen 361105, China
| | - Xingjian Bi
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Science, Xiamen University; Xiamen 361105, China
| | - Hai Yu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Science, Xiamen University; Xiamen 361105, China
| | - Zheng Fu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Science, Xiamen University; Xiamen 361105, China
| | - Xinlin Liu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Science, Xiamen University; Xiamen 361105, China
| | - Shaowei Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Science, Xiamen University; Xiamen 361105, China
| | - Zhiqiang An
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Science, Xiamen University; Xiamen 361105, China
- Texas Therapeutics Institute, The Brown Foundation of Molecular Medicine, University of Texas Health Science Center at Houston, Houston TX77030, USA
| | - Wenxin Luo
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Science, Xiamen University; Xiamen 361105, China
| | - Qinjian Zhao
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Science, Xiamen University; Xiamen 361105, China
| | - Ningshao Xia
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Science, Xiamen University; Xiamen 361105, China
| |
Collapse
|
1019
|
Chowdhury N, Bagchi A. Molecular insight into the activity of LasR protein from Pseudomonas aeruginosa in the regulation of virulence gene expression by this organism. Gene 2016; 580:80-7. [PMID: 26768577 DOI: 10.1016/j.gene.2015.12.067] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 11/09/2015] [Accepted: 12/30/2015] [Indexed: 10/22/2022]
Abstract
Pseudomonas aeruginosa is an opportunistic human pathogen. This organism attacks human patients suffering from diseases like AIDS, cancer, cystic fibrosis, etc. One of the important virulent factors produced by this organism is Hydrogen Cyanide. This is expressed from the genes encoded by the hcnABC operon. The expressions of the genes encoded by hcnABC operon are mediated mainly by the interactions of LasR protein with the corresponding promoter region of the hcnABC operon. The LasR protein acts as a dimer and binds to the promoter DNA with the help of an autoinducer ligand. However, till date the detailed molecular mechanism of how the LasR protein interacts with the promoter DNA is not clearly known. Therefore, in this work, an attempt has been made to analyze the mode of interactions of the LasR protein with the promoter DNA region of the hcnABC operon. We analyzed the three dimensional structure of the LasR protein from Pseudomonas aeruginosa and docked the protein with the autoinducer ligand. We then docked the ligand-bound-LasR-protein as well the LasR-protein-without-the-autoinducer-ligand on to the promoter DNA region of hcnABC operon. We analyzed the details of the interaction profiles of LasR protein with the autoinducer ligand. We also deciphered the details of the LasR promoter-DNA interactions. We compared the modes of DNA bindings by the LasR protein in presence and absence of the autoinducer ligand and tried to analyze the molecular details of the binding of LasR protein with the promoter DNA region of hcnABC operon during hcnABC gene expression. This study may therefore pave the pathway for future experiments to determine the relative effects of the amino acid residues of LasR protein in DNA binding during the transcription of hcnABC operon.
Collapse
Affiliation(s)
- Nilkanta Chowdhury
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, Nadia 741235, India
| | - Angshuman Bagchi
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, Nadia 741235, India.
| |
Collapse
|
1020
|
Rigid-Docking Approaches to Explore Protein-Protein Interaction Space. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 160:33-55. [PMID: 27830312 DOI: 10.1007/10_2016_41] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Protein-protein interactions play core roles in living cells, especially in the regulatory systems. As information on proteins has rapidly accumulated on publicly available databases, much effort has been made to obtain a better picture of protein-protein interaction networks using protein tertiary structure data. Predicting relevant interacting partners from their tertiary structure is a challenging task and computer science methods have the potential to assist with this. Protein-protein rigid docking has been utilized by several projects, docking-based approaches having the advantages that they can suggest binding poses of predicted binding partners which would help in understanding the interaction mechanisms and that comparing docking results of both non-binders and binders can lead to understanding the specificity of protein-protein interactions from structural viewpoints. In this review we focus on explaining current computational prediction methods to predict pairwise direct protein-protein interactions that form protein complexes.
Collapse
|
1021
|
Saha P, Sikdar S, Chakrabarti J, Ghosh M. Response to chemical induced changes and their implication in yfdX proteins. RSC Adv 2016. [DOI: 10.1039/c6ra21913f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
|
1022
|
Dow BA, Davidson VL. Converting the bis-FeIV state of the diheme enzyme MauG to Compound I decreases the reorganization energy for electron transfer. Biochem J 2016; 473:67-72. [PMID: 26494530 PMCID: PMC4860820 DOI: 10.1042/bj20150998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 10/22/2015] [Indexed: 11/17/2022]
Abstract
The electron transfer (ET) properties of two types of high-valent hemes were studied within the same protein matrix; the bis-Fe(IV) state of MauG and the Compound I state of Y294H MauG. The latter is formed as a consequence of mutation of the tyrosine which forms the distal axial ligand of the six-coordinate heme that allows it to stabilize Fe(IV) in the absence of an external ligand. The rates of the ET reaction of each high-valent species with the type I copper protein, amicyanin, were determined at different temperatures and analysed by ET theory. The reaction with bis-Fe(IV) wild-type (WT) MauG exhibited a reorganization energy (λ) that was 0.39 eV greater than that for the reaction of Compound I Y295H MauG. It is concluded that the delocalization of charge over the two hemes in the bis-Fe(IV) state is responsible for the larger λ, relative to the Compound I state in which the Fe(V) equivalent is isolated on one heme. Although the increase in λ decreases the rate of ET, the delocalization of charge decreases the ET distance to its natural substrate protein, thus increasing the ET rate. This describes how proteins can balance different ET properties of complex redox cofactors to optimize each system for its particular ET or catalytic reaction.
Collapse
Affiliation(s)
- Brian A Dow
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32827, U.S.A
| | - Victor L Davidson
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32827, U.S.A.
| |
Collapse
|
1023
|
Song Y, Nelp M, Bandarian V, Wysocki VH. Refining the Structural Model of a Heterohexameric Protein Complex: Surface Induced Dissociation and Ion Mobility Provide Key Connectivity and Topology Information. ACS CENTRAL SCIENCE 2015; 1:477-487. [PMID: 26744735 PMCID: PMC4690985 DOI: 10.1021/acscentsci.5b00251] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Indexed: 05/21/2023]
Abstract
Toyocamycin nitrile hydratase (TNH) is a protein hexamer that catalyzes the hydration of toyocamycin to produce sangivamycin. The structure of hexameric TNH and the arrangement of subunits within the complex, however, have not been solved by NMR or X-ray crystallography. Native mass spectrometry (MS) clearly shows that TNH is composed of two copies each of the α, β, and γ subunits. Previous surface induced dissociation (SID) tandem mass spectrometry on a quadrupole time-of-flight (QTOF) platform suggests that the TNH hexamer is a dimer composed of two αβγ trimers; furthermore, the results suggest that α-β interact most strongly (Blackwell et al. Anal. Chem. 2011, 83, 2862-2865). Here, multiple complementary MS based approaches and homology modeling have been applied to refine the structure of TNH. Solution-phase organic solvent disruption coupled with native MS agrees with the previous SID results. By coupling surface induced dissociation with ion mobility mass spectrometry (SID/IM), further information on the intersubunit contacts and relative interfacial strengths are obtained. The results show that TNH is a dimer of αβγ trimers, that within the trimer the α, β subunits bind most strongly, and that the primary contact between the two trimers is through a γ-γ interface. Collisional cross sections (CCSs) measured from IM experiments are used as constraints for postulating the arrangement of the subunits represented by coarse-grained spheres. Covalent labeling (surface mapping) together with protein complex homology modeling and docking of trimers to form hexamer are utilized with all the above information to propose the likely quaternary structure of TNH, with chemical cross-linking providing cross-links consistent with the proposed structure. The novel feature of this approach is the use of SID-MS with ion mobility to define complete connectivity and relative interfacial areas of a heterohexameric protein complex, providing much more information than is available from solution disruption. That information, when combined with CCS-guided coarse-grained modeling and covalent labeling restraints for homology modeling and trimer-trimer docking, provides atomic models of a previously uncharacterized heterohexameric protein complex.
Collapse
Affiliation(s)
- Yang Song
- Department
of Chemistry and Biochemistry, The Ohio
State University, Columbus, Ohio 43210, United States
| | - Micah
T. Nelp
- Department
of Chemistry and Biochemistry, The University
of Arizona, Tucson, Arizona 85721, United
States
- Department
of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Vahe Bandarian
- Department
of Chemistry and Biochemistry, The University
of Arizona, Tucson, Arizona 85721, United
States
- Department
of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Vicki H. Wysocki
- Department
of Chemistry and Biochemistry, The Ohio
State University, Columbus, Ohio 43210, United States
- Address: 260 Biomedical Research
Tower, 460 West 12th Avenue, Columbus, OH 43210, USA. Phone: 614-292-8687. E-mail:
| |
Collapse
|
1024
|
Structural and functional interactions between six-transmembrane μ-opioid receptors and β2-adrenoreceptors modulate opioid signaling. Sci Rep 2015; 5:18198. [PMID: 26657998 PMCID: PMC4676002 DOI: 10.1038/srep18198] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 11/11/2015] [Indexed: 12/20/2022] Open
Abstract
The primary molecular target for clinically used opioids is the μ-opioid receptor (MOR). Besides the major seven-transmembrane (7TM) receptors, the MOR gene codes for alternatively spliced six-transmembrane (6TM) isoforms, the biological and clinical significance of which remains unclear. Here, we show that the otherwise exclusively intracellular localized 6TM-MOR translocates to the plasma membrane upon coexpression with β2-adrenergic receptors (β2-ARs) through an interaction with the fifth and sixth helices of β2-AR. Coexpression of the two receptors in BE(2)-C neuroblastoma cells potentiates calcium responses to a 6TM-MOR ligand, and this calcium response is completely blocked by a selective β2-antagonist in BE(2)-C cells, and in trigeminal and dorsal root ganglia. Co-administration of 6TM-MOR and β2-AR ligands leads to substantial analgesic synergy and completely reverses opioid-induced hyperalgesia in rodent behavioral models. Together, our results provide evidence that the heterodimerization of 6TM-MOR with β2-AR underlies a molecular mechanism for 6TM cellular signaling, presenting a unique functional responses to opioids. This signaling pathway may contribute to the hyperalgesic effects of opioids that can be efficiently blocked by β2-AR antagonists, providing a new avenue for opioid therapy.
Collapse
|
1025
|
Maklashina E, Rajagukguk S, Starbird CA, McDonald WH, Koganitsky A, Eisenbach M, Iverson TM, Cecchini G. Binding of the Covalent Flavin Assembly Factor to the Flavoprotein Subunit of Complex II. J Biol Chem 2015; 291:2904-16. [PMID: 26644464 DOI: 10.1074/jbc.m115.690396] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Indexed: 01/23/2023] Open
Abstract
Escherichia coli harbors two highly conserved homologs of the essential mitochondrial respiratory complex II (succinate:ubiquinone oxidoreductase). Aerobically the bacterium synthesizes succinate:quinone reductase as part of its respiratory chain, whereas under microaerophilic conditions, the quinol:fumarate reductase can be utilized. All complex II enzymes harbor a covalently bound FAD co-factor that is essential for their ability to oxidize succinate. In eukaryotes and many bacteria, assembly of the covalent flavin linkage is facilitated by a small protein assembly factor, termed SdhE in E. coli. How SdhE assists with formation of the covalent flavin bond and how it binds the flavoprotein subunit of complex II remain unknown. Using photo-cross-linking, we report the interaction site between the flavoprotein of complex II and the SdhE assembly factor. These data indicate that SdhE binds to the flavoprotein between two independently folded domains and that this binding mode likely influences the interdomain orientation. In so doing, SdhE likely orients amino acid residues near the dicarboxylate and FAD binding site, which facilitates formation of the covalent flavin linkage. These studies identify how the conserved SdhE assembly factor and its homologs participate in complex II maturation.
Collapse
Affiliation(s)
- Elena Maklashina
- From the Molecular Biology Division, Veterans Affairs Medical Center, San Francisco, California 94121, the Department of Biochemistry & Biophysics, University of California, San Francisco, California 94158
| | - Sany Rajagukguk
- From the Molecular Biology Division, Veterans Affairs Medical Center, San Francisco, California 94121
| | | | - W Hayes McDonald
- the Department of Biochemistry and Mass Spectrometry Research Center
| | - Anna Koganitsky
- the Department of Biological Chemistry, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Michael Eisenbach
- the Department of Biological Chemistry, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Tina M Iverson
- the Department of Biochemistry and Mass Spectrometry Research Center, the Department of Pharmacology, the Center for Structural Biology, and the Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232, and
| | - Gary Cecchini
- From the Molecular Biology Division, Veterans Affairs Medical Center, San Francisco, California 94121, the Department of Biochemistry & Biophysics, University of California, San Francisco, California 94158,
| |
Collapse
|
1026
|
Qiu YL, He QH, Xu Y, Wang W, Liu YY. Modification of a deoxynivalenol-antigen-mimicking nanobody to improve immunoassay sensitivity by site-saturation mutagenesis. Anal Bioanal Chem 2015; 408:895-903. [PMID: 26608283 DOI: 10.1007/s00216-015-9181-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 10/27/2015] [Accepted: 11/09/2015] [Indexed: 01/28/2023]
Abstract
A nanobody (N-28) which can act as a deoxynivalenol (DON) antigen has been generated, and its residues Thr102-Ser106 were identified to bind with anti-DON monoclonal antibody by alanine-scanning mutagenesis. Site-saturation mutagenesis was used to analyze the plasticity of five residues and to improve the sensitivity of the N-28-based immunoassay. After mutagenesis, three mutants were selected by phage immunoassay and were sequenced. The half-maximal inhibitory concentrations of the immunoassay based on mutants N-28-T102Y, N-28-V103L, and N-28-Y105F were 24.49 ± 1.0, 51.83 ± 2.5, and 35.65 ± 1.6 ng/mL, respectively, showing the assay was, respectively, 3.2, 1.5, and 2.2 times more sensitive than the wild-type-based assay. The best mutant, N-28-T102Y, was used to develop a competitive phage ELISA to detect DON in cereals with high specificity and accuracy. In addition, the structural properties of N-28-T102Y and N-28 were investigated, revealing that the affinity of N-28-T102Y decreased because of increased steric hindrance with the large side chain. The lower-binding-affinity antigen mimetic may contribute to the improvement of the sensitivity of competitive immunoassays. These results demonstrate that nanobodies would be a favorable tool for engineering. Moreover, our results have laid a solid foundation for site-saturation mutagenesis of antigen-mimicking nanobodies to improve immunoassay sensitivity for small molecules.
Collapse
Affiliation(s)
- Yu-Lou Qiu
- State Key Laboratory of Food Science and Technology, Sino-German Joint Research Institute, Nanchang University, No. 235 Nanjing East Road, Nanchang, 330047, China
| | - Qing-Hua He
- State Key Laboratory of Food Science and Technology, Sino-German Joint Research Institute, Nanchang University, No. 235 Nanjing East Road, Nanchang, 330047, China.
| | - Yang Xu
- State Key Laboratory of Food Science and Technology, Sino-German Joint Research Institute, Nanchang University, No. 235 Nanjing East Road, Nanchang, 330047, China.
| | - Wei Wang
- State Key Laboratory of Food Science and Technology, Sino-German Joint Research Institute, Nanchang University, No. 235 Nanjing East Road, Nanchang, 330047, China
| | - Yuan-Yuan Liu
- State Key Laboratory of Food Science and Technology, Sino-German Joint Research Institute, Nanchang University, No. 235 Nanjing East Road, Nanchang, 330047, China
| |
Collapse
|
1027
|
Letko M, Booiman T, Kootstra N, Simon V, Ooms M. Identification of the HIV-1 Vif and Human APOBEC3G Protein Interface. Cell Rep 2015; 13:1789-99. [PMID: 26628364 DOI: 10.1016/j.celrep.2015.10.068] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 10/07/2015] [Accepted: 10/21/2015] [Indexed: 02/02/2023] Open
Abstract
Human cells express natural antiviral proteins, such as APOBEC3G (A3G), that potently restrict HIV replication. As a counter-defense, HIV encodes the accessory protein Vif, which binds A3G and mediates its proteasomal degradation. Our structural knowledge on how Vif and A3G interact is limited, because a co-structure is not available. We identified specific points of contact between Vif and A3G by using functional assays with full-length A3G, patient-derived Vif variants, and HIV forced evolution. These anchor points were used to model and validate the Vif-A3G interface. The resultant co-structure model shows that the negatively charged β4-α4 A3G loop, which contains primate-specific variation, is the core Vif binding site and forms extensive interactions with a positively charged pocket in HIV Vif. Our data present a functional map of this viral-host interface and open avenues for targeted approaches to block HIV replication by obstructing the Vif-A3G interaction.
Collapse
Affiliation(s)
- Michael Letko
- The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Thijs Booiman
- Department of Experimental Immunology, Academic Medical Center, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands
| | - Neeltje Kootstra
- Department of Experimental Immunology, Academic Medical Center, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands
| | - Viviana Simon
- The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Marcel Ooms
- The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| |
Collapse
|
1028
|
Simonov AN, Holien JK, Yeung JCI, Nguyen AD, Corbin CJ, Zheng J, Kuznetsov VL, Auchus RJ, Conley AJ, Bond AM, Parker MW, Rodgers RJ, Martin LL. Mechanistic Scrutiny Identifies a Kinetic Role for Cytochrome b5 Regulation of Human Cytochrome P450c17 (CYP17A1, P450 17A1). PLoS One 2015; 10:e0141252. [PMID: 26587646 PMCID: PMC4654539 DOI: 10.1371/journal.pone.0141252] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 10/06/2015] [Indexed: 01/12/2023] Open
Abstract
Cytochrome P450c17 (P450 17A1, CYP17A1) is a critical enzyme in the synthesis of androgens and is now a target enzyme for the treatment of prostate cancer. Cytochrome P450c17 can exhibit either one or two physiological enzymatic activities differentially regulated by cytochrome b5. How this is achieved remains unknown. Here, comprehensive in silico, in vivo and in vitro analyses were undertaken. Fluorescence Resonance Energy Transfer analysis showed close interactions within living cells between cytochrome P450c17 and cytochrome b5. In silico modeling identified the sites of interaction and confirmed that E48 and E49 residues in cytochrome b5 are essential for activity. Quartz crystal microbalance studies identified specific protein-protein interactions in a lipid membrane. Voltammetric analysis revealed that the wild type cytochrome b5, but not a mutated, E48G/E49G cyt b5, altered the kinetics of electron transfer between the electrode and the P450c17. We conclude that cytochrome b5 can influence the electronic conductivity of cytochrome P450c17 via allosteric, protein-protein interactions.
Collapse
Affiliation(s)
| | - Jessica K. Holien
- ACRF Rational Drug Discovery Centre, St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia
| | | | - Ann D. Nguyen
- School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - C. Jo Corbin
- School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - Jie Zheng
- Department of Physiology and Membrane Biology, School of Medicine, University of California Davis, Davis, California, United States of America
| | | | - Richard J. Auchus
- Division of Metabolism, Endocrinology and Diabetes, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Alan J. Conley
- School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - Alan M. Bond
- School of Chemistry, Monash University, Clayton, Victoria, Australia
| | - Michael W. Parker
- ACRF Rational Drug Discovery Centre, St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Raymond J. Rodgers
- Discipline of Obstetrics and Gynaecology, School of Paediatrics and Reproductive Health, Robinson Research Institute, University of Adelaide, Adelaide, South Australia, Australia
| | | |
Collapse
|
1029
|
Tadepalli S, Kuang Z, Jiang Q, Liu KK, Fisher MA, Morrissey JJ, Kharasch ED, Slocik JM, Naik RR, Singamaneni S. Peptide Functionalized Gold Nanorods for the Sensitive Detection of a Cardiac Biomarker Using Plasmonic Paper Devices. Sci Rep 2015; 5:16206. [PMID: 26552720 PMCID: PMC4639779 DOI: 10.1038/srep16206] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 09/16/2015] [Indexed: 12/13/2022] Open
Abstract
The sensitivity of localized surface plasmon resonance (LSPR) of metal nanostructures to adsorbates lends itself to a powerful class of label-free biosensors. Optical properties of plasmonic nanostructures are dependent on the geometrical features and the local dielectric environment. The exponential decay of the sensitivity from the surface of the plasmonic nanotransducer calls for the careful consideration in its design with particular attention to the size of the recognition and analyte layers. In this study, we demonstrate that short peptides as biorecognition elements (BRE) compared to larger antibodies as target capture agents offer several advantages. Using a bioplasmonic paper device (BPD), we demonstrate the selective and sensitive detection of the cardiac biomarker troponin I (cTnI). The smaller sized peptide provides higher sensitivity and a lower detection limit using a BPD. Furthermore, the excellent shelf-life and thermal stability of peptide-based LSPR sensors, which precludes the need for special storage conditions, makes it ideal for use in resource-limited settings.
Collapse
Affiliation(s)
- Sirimuvva Tadepalli
- Institute of Material Science and Engineering and Department of Mechanical Engineering and Material Science, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Zhifeng Kuang
- Soft Matter Materials Branch, Materials and Manufacturing Directorate, Wright Patterson Air Force Base, Dayton, OH 45433, USA
| | - Qisheng Jiang
- Institute of Material Science and Engineering and Department of Mechanical Engineering and Material Science, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Keng-Ku Liu
- Institute of Material Science and Engineering and Department of Mechanical Engineering and Material Science, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Marilee A. Fisher
- Department of Anesthesiology, Division of Clinical and Translational Research, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Jeremiah J. Morrissey
- Department of Anesthesiology, Division of Clinical and Translational Research, Washington University in St. Louis, St. Louis, MO 63110, USA
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Evan D. Kharasch
- Department of Anesthesiology, Division of Clinical and Translational Research, Washington University in St. Louis, St. Louis, MO 63110, USA
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Joseph M. Slocik
- Soft Matter Materials Branch, Materials and Manufacturing Directorate, Wright Patterson Air Force Base, Dayton, OH 45433, USA
| | - Rajesh R. Naik
- Soft Matter Materials Branch, Materials and Manufacturing Directorate, Wright Patterson Air Force Base, Dayton, OH 45433, USA
| | - Srikanth Singamaneni
- Institute of Material Science and Engineering and Department of Mechanical Engineering and Material Science, Washington University in St. Louis, St. Louis, MO, 63130, USA
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| |
Collapse
|
1030
|
Peptide Functionalized Gold Nanorods for the Sensitive Detection of a Cardiac Biomarker Using Plasmonic Paper Devices. Sci Rep 2015. [DOI: 10.1038/srep1620610.1038/srep16206] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
|
1031
|
Juntapremjit S, Thamwiriyasati N, Kurehong C, Prangkio P, Shank L, Powthongchin B, Angsuthanasombat C. Functional importance of the Gly cluster in transmembrane helix 2 of the Bordetella pertussis CyaA-hemolysin: Implications for toxin oligomerization and pore formation. Toxicon 2015; 106:14-9. [DOI: 10.1016/j.toxicon.2015.09.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 08/07/2015] [Accepted: 09/07/2015] [Indexed: 10/23/2022]
|
1032
|
Fayaz SM, Rajanikant GK. Modelling the molecular mechanism of protein-protein interactions and their inhibition: CypD-p53 case study. Mol Divers 2015; 19:931-43. [PMID: 26170095 DOI: 10.1007/s11030-015-9612-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 07/01/2015] [Indexed: 02/06/2023]
Abstract
Cyclophilin D (CypD) is an important regulatory protein involved in mitochondrial membrane permeability transition and cell death. Further, the mitochondrial CypD-p53 axis is an important contributor to necroptosis, a form of programmed necrosis, involved in various cardiovascular and neurological disorders. The CypD ligand, Cyclosporin A (CsA), was identified as an inhibitor of this interaction. In this study, using computational methods, we have attempted to model the CypD-p53 interaction in order to delineate their mode of binding and also to disclose the molecular mechanism, by means of which CsA interferes with this interaction. It was observed that p53 binds at the CsA-binding site of CypD. The knowledge obtained from this modelling was employed to identify novel CypD inhibitors through structure-based methods. Further, the identified compounds were tested by a similar strategy, adopted during the modelling process. This strategy could be applied to study the mechanism of protein-protein interaction (PPI) inhibition and to identify novel PPI inhibitors.
Collapse
Affiliation(s)
- S M Fayaz
- School of Biotechnology, National Institute of Technology Calicut, Calicut, 673601, India
| | - G K Rajanikant
- School of Biotechnology, National Institute of Technology Calicut, Calicut, 673601, India.
| |
Collapse
|
1033
|
Dong L, Tan Q, Ye W, Liu D, Chen H, Hu H, Wen D, Liu Y, Cao Y, Kang J, Fan J, Guo W, Wu W. Screening and Identifying a Novel ssDNA Aptamer against Alpha-fetoprotein Using CE-SELEX. Sci Rep 2015; 5:15552. [PMID: 26497223 PMCID: PMC4620443 DOI: 10.1038/srep15552] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 09/28/2015] [Indexed: 01/01/2023] Open
Abstract
Alpha-fetoprotein (AFP) is a liver cancer associated protein and has long been utilized as a serum tumor biomarker of disease progression. AFP is usually detected in HCC patients by an antibody based system. Recently, however, aptamers generated from systematic evolution of ligands by exponential enrichment (SELEX) were reported to have an alternative potential in targeted imaging, diagnosis and therapy. In this study, AFP-bound ssDNA aptamers were screened and identified using capillary electrophoresis (CE) SELEX technology. After cloning, sequencing and motif analysis, we successfully confirmed an aptamer, named AP273, specifically targeting AFP. The aptamer could be used as a probe in AFP immunofluorescence imaging in HepG2, one AFP positive cancer cell line, but not in A549, an AFP negative cancer cell line. More interesting, the aptamer efficiently inhibited the migration and invasion of HCC cells after in vivo transfection. Motif analysis revealed that AP273 had several stable secondary motifs in its structure. Our results indicate that CE-SELEX technology is an efficient method to screen specific protein-bound ssDNA, and AP273 could be used as an agent in AFP-based staining, diagnosis and therapy, although more works are still needed.
Collapse
Affiliation(s)
- Lili Dong
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China
| | - Qiwen Tan
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Wei Ye
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Dongli Liu
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China
| | - Haifeng Chen
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hongwei Hu
- Shanghai Aijin Biochemical Science &Technology Co. Ltd., Shanghai 200336, China
| | - Duo Wen
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China
| | - Yang Liu
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China
| | - Ya Cao
- Cancer Research Institute, Xiangya School of Medicine, Central South University, Key Laboratory of Chinese Ministry of Education, Changsha 410078, China
| | - Jingwu Kang
- Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jia Fan
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China.,Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Wei Guo
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Weizhong Wu
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China
| |
Collapse
|
1034
|
Orekhov PS, Klose D, Mulkidjanian AY, Shaitan KV, Engelhard M, Klare JP, Steinhoff HJ. Signaling and Adaptation Modulate the Dynamics of the Photosensoric Complex of Natronomonas pharaonis. PLoS Comput Biol 2015; 11:e1004561. [PMID: 26496122 PMCID: PMC4651059 DOI: 10.1371/journal.pcbi.1004561] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 09/18/2015] [Indexed: 11/19/2022] Open
Abstract
Motile bacteria and archaea respond to chemical and physical stimuli seeking optimal conditions for survival. To this end transmembrane chemo- and photoreceptors organized in large arrays initiate signaling cascades and ultimately regulate the rotation of flagellar motors. To unravel the molecular mechanism of signaling in an archaeal phototaxis complex we performed coarse-grained molecular dynamics simulations of a trimer of receptor/transducer dimers, namely NpSRII/NpHtrII from Natronomonas pharaonis. Signaling is regulated by a reversible methylation mechanism called adaptation, which also influences the level of basal receptor activation. Mimicking two extreme methylation states in our simulations we found conformational changes for the transmembrane region of NpSRII/NpHtrII which resemble experimentally observed light-induced changes. Further downstream in the cytoplasmic domain of the transducer the signal propagates via distinct changes in the dynamics of HAMP1, HAMP2, the adaptation domain and the binding region for the kinase CheA, where conformational rearrangements were found to be subtle. Overall these observations suggest a signaling mechanism based on dynamic allostery resembling models previously proposed for E. coli chemoreceptors, indicating similar properties of signal transduction for archaeal photoreceptors and bacterial chemoreceptors. Achaea and bacteria can “see” and “sniffle”, they have photo- and chemosensors that measure the environment. On the cell poles, these sensor proteins form large arrays built of several thousands of different receptors. The receptors comprise extracellular or transmembrane sensory domains and elongated homodimeric coiled-coil bundles, which transduce the signals from the membrane across ~20 nm to a conserved cytoplasmic signaling subdomain in an unknown manner. In our study we performed coarse-grained molecular dynamics simulations of the phototactic receptor/transducer complex from Natronomonas pharaonis. Comparing fully methylated and demethylated complexes reveals an interconversion between states of different dynamics along the coiled-coil bundle, which might represent the essential characteristics of the signal transfer from the membrane to the binding sites of the downstream kinase CheA.
Collapse
Affiliation(s)
- Philipp S. Orekhov
- Department of Physics, University of Osnabrueck, Osnabrueck, Germany
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Daniel Klose
- Department of Physics, University of Osnabrueck, Osnabrueck, Germany
| | - Armen Y. Mulkidjanian
- Department of Physics, University of Osnabrueck, Osnabrueck, Germany
- Department of Bioengineering and Bioinformatics and A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | | | - Martin Engelhard
- Max-Planck-Institute for Molecular Physiology, Dortmund, Germany
| | - Johann P. Klare
- Department of Physics, University of Osnabrueck, Osnabrueck, Germany
| | | |
Collapse
|
1035
|
Ajamian L, Abel K, Rao S, Vyboh K, García-de-Gracia F, Soto-Rifo R, Kulozik AE, Gehring NH, Mouland AJ. HIV-1 Recruits UPF1 but Excludes UPF2 to Promote Nucleocytoplasmic Export of the Genomic RNA. Biomolecules 2015; 5:2808-39. [PMID: 26492277 PMCID: PMC4693258 DOI: 10.3390/biom5042808] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 09/09/2015] [Accepted: 09/16/2015] [Indexed: 12/11/2022] Open
Abstract
Unspliced, genomic HIV-1 RNA (vRNA) is a component of several ribonucleoprotein complexes (RNP) during the viral replication cycle. In earlier work, we demonstrated that the host upframeshift protein 1 (UPF1), a key factor in nonsense-mediated mRNA decay (NMD), colocalized and associated to the viral structural protein Gag during viral egress. In this work, we demonstrate a new function for UPF1 in the regulation of vRNA nuclear export. OPEN ACCESS Biomolecules 2015, 5 2809 We establish that the nucleocytoplasmic shuttling of UPF1 is required for this function and demonstrate that UPF1 exists in two essential viral RNPs during the late phase of HIV-1 replication: the first, in a nuclear export RNP that contains Rev, CRM1, DDX3 and the nucleoporin p62, and the second, which excludes these nuclear export markers but contains Gag in the cytoplasm. Interestingly, we observed that both UPF2 and the long isoform of UPF3a, UPF3aL, but not the shorter isoforms UPF3aS and UPF3b, are excluded from the UPF1-Rev-CRM1-DDX3 complex as they are negative regulators of vRNA nuclear export. In silico protein-protein docking analyses suggest that Rev binds UPF1 in a region that overlaps the UPF2 binding site, thus explaining the exclusion of this negative regulatory factor by HIV-1 that is necessary for vRNA trafficking. This work uncovers a novel and unique regulatory circuit involving several UPF proteins that ultimately regulate vRNA nuclear export and trafficking.
Collapse
Affiliation(s)
- Lara Ajamian
- HIV-1 RNA Trafficking Laboratory, Lady Davis Institute for Medical Research-Sir Mortimer B. Davis Jewish General Hospital, Montréal QC H3T 1E2, Canada.
- Department of Medicine, Division of Experimental Medicine, McGill University, Montréal QC H3A 2B4, Canada.
| | - Karen Abel
- HIV-1 RNA Trafficking Laboratory, Lady Davis Institute for Medical Research-Sir Mortimer B. Davis Jewish General Hospital, Montréal QC H3T 1E2, Canada.
- Department of Microbiology and Immunology, McGill University, Montréal QC H3T 1E2, Canada.
| | - Shringar Rao
- HIV-1 RNA Trafficking Laboratory, Lady Davis Institute for Medical Research-Sir Mortimer B. Davis Jewish General Hospital, Montréal QC H3T 1E2, Canada.
- Department of Microbiology and Immunology, McGill University, Montréal QC H3T 1E2, Canada.
| | - Kishanda Vyboh
- HIV-1 RNA Trafficking Laboratory, Lady Davis Institute for Medical Research-Sir Mortimer B. Davis Jewish General Hospital, Montréal QC H3T 1E2, Canada.
- Department of Microbiology and Immunology, McGill University, Montréal QC H3T 1E2, Canada.
| | - Francisco García-de-Gracia
- Laboratory of Molecular and Cellular Virology, Virology Program, Biomedical Sciences Institute, Faculty of Medicine, Universidad de Chile, Independencia 8389100, Santiago, Chile.
| | - Ricardo Soto-Rifo
- Laboratory of Molecular and Cellular Virology, Virology Program, Biomedical Sciences Institute, Faculty of Medicine, Universidad de Chile, Independencia 8389100, Santiago, Chile.
| | - Andreas E Kulozik
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg 69120, Germany.
- European Molecular Biology Laboratory, Partnership Unit, University of Heidelberg Molecular Medicine, Heidelberg 69117, Germany.
| | - Niels H Gehring
- Institute for Genetics, University of Cologne, Cologne 50674, Germany.
| | - Andrew J Mouland
- HIV-1 RNA Trafficking Laboratory, Lady Davis Institute for Medical Research-Sir Mortimer B. Davis Jewish General Hospital, Montréal QC H3T 1E2, Canada.
- Department of Medicine, Division of Experimental Medicine, McGill University, Montréal QC H3A 2B4, Canada.
- Department of Microbiology and Immunology, McGill University, Montréal QC H3T 1E2, Canada.
| |
Collapse
|
1036
|
Froese DS, Kopec J, Fitzpatrick F, Schuller M, McCorvie TJ, Chalk R, Plessl T, Fettelschoss V, Fowler B, Baumgartner MR, Yue WW. Structural Insights into the MMACHC-MMADHC Protein Complex Involved in Vitamin B12 Trafficking. J Biol Chem 2015; 290:29167-77. [PMID: 26483544 PMCID: PMC4705923 DOI: 10.1074/jbc.m115.683268] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Indexed: 11/06/2022] Open
Abstract
Conversion of vitamin B12 (cobalamin, Cbl) into the cofactor forms methyl-Cbl (MeCbl) and adenosyl-Cbl (AdoCbl) is required for the function of two crucial enzymes, mitochondrial methylmalonyl-CoA mutase and cytosolic methionine synthase, respectively. The intracellular proteins MMACHC and MMADHC play important roles in processing and targeting the Cbl cofactor to its destination enzymes, and recent evidence suggests that they may interact while performing these essential trafficking functions. To better understand the molecular basis of this interaction, we have mapped the crucial protein regions required, indicate that Cbl is likely processed by MMACHC prior to interaction with MMADHC, and identify patient mutations on both proteins that interfere with complex formation, via different mechanisms. We further report the crystal structure of the MMADHC C-terminal region at 2.2 Å resolution, revealing a modified nitroreductase fold with surprising homology to MMACHC despite their poor sequence conservation. Because MMADHC demonstrates no known enzymatic activity, we propose it as the first protein known to repurpose the nitroreductase fold solely for protein-protein interaction. Using small angle x-ray scattering, we reveal the MMACHC-MMADHC complex as a 1:1 heterodimer and provide a structural model of this interaction, where the interaction region overlaps with the MMACHC-Cbl binding site. Together, our findings provide novel structural evidence and mechanistic insight into an essential biological process, whereby an intracellular "trafficking chaperone" highly specific for a trace element cofactor functions via protein-protein interaction, which is disrupted by inherited disease mutations.
Collapse
Affiliation(s)
- D Sean Froese
- From the Division of Metabolism and Children's Research Center, University Children's, Hospital, CH-8032 Zurich, Switzerland, radiz - Rare Disease Initiative Zurich, Clinical Research Priority Program for Rare Diseases, University of Zurich, CH-8032 Zurich, Switzerland
| | - Jolanta Kopec
- the Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom, and
| | - Fiona Fitzpatrick
- the Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom, and
| | - Marion Schuller
- the Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom, and
| | - Thomas J McCorvie
- the Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom, and
| | - Rod Chalk
- the Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom, and
| | - Tanja Plessl
- From the Division of Metabolism and Children's Research Center, University Children's, Hospital, CH-8032 Zurich, Switzerland
| | - Victoria Fettelschoss
- From the Division of Metabolism and Children's Research Center, University Children's, Hospital, CH-8032 Zurich, Switzerland
| | - Brian Fowler
- From the Division of Metabolism and Children's Research Center, University Children's, Hospital, CH-8032 Zurich, Switzerland
| | - Matthias R Baumgartner
- From the Division of Metabolism and Children's Research Center, University Children's, Hospital, CH-8032 Zurich, Switzerland, radiz - Rare Disease Initiative Zurich, Clinical Research Priority Program for Rare Diseases, University of Zurich, CH-8032 Zurich, Switzerland, the Zurich Center for Integrative Human Physiology, University of Zurich, 8057 Zurich, Switzerland
| | - Wyatt W Yue
- the Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom, and
| |
Collapse
|
1037
|
Basu A, Das A, Mondal A, Datta S. Structural analysis of inter-genus complexes of V-antigen and its regulator and their stabilization by divalent metal ions. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2015; 45:113-28. [PMID: 26463823 DOI: 10.1007/s00249-015-1081-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 09/09/2015] [Accepted: 09/16/2015] [Indexed: 10/23/2022]
Abstract
Gram-negative bacteria like Yersinia, Pseudomonas, and Aeromonas need type III secretion system (T3SS) for their pathogenicity. V-antigen and its regulator are essential for functioning of T3SS. There is significant functional conservation amongst V-antigen and its regulator belonging to the Ysc family. In this study, we have structurally characterized the inter-genus complexes of V-antigen and its regulator. ConSurf analysis demonstrates that V-antigens belonging to the Ysc family show high structural identity predominantly confined to the two long helical regions. The regulator of V-antigen shows high conservation in its first intramolecular coiled-coil domain, responsible for interaction with V-antigen. ∆LcrG(1-70) localizes within the groove formed by long helices of LcrV, as observed in PcrV-∆PcrG(13-72) interaction. Inter-genus complexes of LcrV-PcrG and PcrV-LcrG exhibited elongated conformation and 1:1 heterodimeric state like the native complex of PcrV-PcrG and LcrV-LcrG. Both native and inter-genus complexes showed rigid tertiary structure, solvent-exposed hydrophobic patches, and cooperative melting behavior with high melting temperature. LcrV-PcrG and PcrV-LcrG showed nanomolar affinity of interaction, identical to PcrV-PcrG interaction, but stronger than LcrV-LcrG interaction. Calcium (a secretion blocker of T3SS) propels all the complexes towards a highly monodisperse form. Calcium and magnesium increase the helicity of the native and inter-genus complexes, and causes helix-helix stabilization. Stabilization of helices leads to a slight increase in the melting temperature by 1.5-2.0 °C. However, calcium does not alter the affinity of interaction of V-antigen and its regulator, emphasizing the effect of divalent of cations at the structural level without any regulatory implications. Therefore, the structural conservation of these inter-genus complexes could be the basis for their functional complementation.
Collapse
Affiliation(s)
- Abhishek Basu
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata, 700032, West Bengal, India
| | - Atanu Das
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata, 700032, West Bengal, India
| | - Abhisek Mondal
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata, 700032, West Bengal, India
| | - Saumen Datta
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata, 700032, West Bengal, India.
| |
Collapse
|
1038
|
Dikhit MR, Kumar S, Vijaymahantesh, Sahoo BR, Mansuri R, Amit A, Yousuf Ansari M, Sahoo GC, Bimal S, Das P. Computational elucidation of potential antigenic CTL epitopes in Ebola virus. INFECTION GENETICS AND EVOLUTION 2015; 36:369-375. [PMID: 26462623 DOI: 10.1016/j.meegid.2015.10.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 09/02/2015] [Accepted: 10/09/2015] [Indexed: 11/28/2022]
Abstract
Cell-mediated immunity is important for the control of Ebola virus infection. We hypothesized that those HLA A0201 and HLA B40 restricted epitopes derived from Ebola virus proteins, would mount a good antigenic response. Here we employed an immunoinformatics approach to identify specific 9mer amino acid which may be capable of inducing a robust cell-mediated immune response in humans. We identified a set of 28 epitopes that had no homologs in humans. Specifically, the epitopes derived from NP, RdRp, GP and VP40 share population coverage of 93.40%, 84.15%, 74.94% and 77.12%, respectively. Based on the other HLA binding specificity and population coverage, seven novel promiscuous epitopes were identified. These 7 promiscuous epitopes from NP, RdRp and GP were found to have world-wide population coverage of more than 95% indicating their potential significance as useful candidates for vaccine design. Epitope conservancy analysis also suggested that most of the peptides are highly conserved (100%) in other virulent Ebola strain (Mayinga-76, Kikwit-95 and Makona-G3816- 2014) and can therefore be further investigated for their immunological relevance and usefulness as vaccine candidates.
Collapse
Affiliation(s)
- Manas R Dikhit
- Department of Bioinformatics, Rajendra Memorial Research Institute of Medical Sciences, Patna 800007, India
| | - Santosh Kumar
- Department of Biotechnology and Department of Pharmacoinformatics, National Institutes of Pharmaceutical Education and Research, Hajipur 844102, India
| | - Vijaymahantesh
- Department of Biotechnology and Department of Pharmacoinformatics, National Institutes of Pharmaceutical Education and Research, Hajipur 844102, India; Division of Immunology, Rajendra Memorial Research Institute of Medical Sciences, Patna 800007, India
| | - Bikash R Sahoo
- Institute for Protein Research, Osaka University, Suita 5650871, Japan
| | - Rani Mansuri
- Department of Bioinformatics, Rajendra Memorial Research Institute of Medical Sciences, Patna 800007, India; Department of Biotechnology and Department of Pharmacoinformatics, National Institutes of Pharmaceutical Education and Research, Hajipur 844102, India
| | - Ajay Amit
- Division of Immunology, Rajendra Memorial Research Institute of Medical Sciences, Patna 800007, India
| | - Md Yousuf Ansari
- Department of Bioinformatics, Rajendra Memorial Research Institute of Medical Sciences, Patna 800007, India; Department of Biotechnology and Department of Pharmacoinformatics, National Institutes of Pharmaceutical Education and Research, Hajipur 844102, India
| | - Ganesh C Sahoo
- Department of Bioinformatics, Rajendra Memorial Research Institute of Medical Sciences, Patna 800007, India
| | - Sanjiva Bimal
- Division of Immunology, Rajendra Memorial Research Institute of Medical Sciences, Patna 800007, India
| | - Pradeep Das
- Dept. of Molecular Parasitology, Rajendra Memorial Research Institute of Medical Sciences, Patna 800007, India.
| |
Collapse
|
1039
|
Abstract
It is long known that peptide neurotoxins derived from a diversity of venomous animals evolve by positive selection following gene duplication, yet a force that drives their adaptive evolution remains a mystery. By using maximum-likelihood models of codon substitution, we analyzed molecular adaptation in scorpion sodium channel toxins from a specific species and found ten positively selected sites, six of which are located at the core-domain of scorpion α-toxins, a region known to interact with two adjacent loops in the voltage-sensor domain (DIV) of sodium channels, as validated by our newly constructed computational model of toxin-channel complex. Despite the lack of positive selection signals in these two loops, they accumulated extensive sequence variations by relaxed purifying selection in prey and predators of scorpions. The evolutionary variability in the toxin-bound regions of sodium channels indicates that accelerated substitutions in the multigene family of scorpion toxins is a consequence of dealing with the target diversity. This work presents an example of atypical co-evolution between animal toxins and their molecular targets, in which toxins suffered from more prominent selective pressure from the channels of their competitors. Our discovery helps explain the evolutionary rationality of gene duplication of toxins in a specific venomous species.
Collapse
|
1040
|
Chen L, Li C, Zhu Y. The HGF inhibitory peptide HGP-1 displays promising in vitro and in vivo efficacy for targeted cancer therapy. Oncotarget 2015; 6:30088-101. [PMID: 26254225 PMCID: PMC4745783 DOI: 10.18632/oncotarget.3937] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 04/28/2015] [Indexed: 12/15/2022] Open
Abstract
HGF/MET pathway mediates cancer initiation and development. Thus, inhibition on HGF-initiated MET signaling pathway would provide a new approach to cancer targeted therapeutics. In our study, we identified a targeting peptide candidate binding to HGF which was named HGF binding peptide-1 (HGP-1) via bacterial surface display methods coupled with fluorescence-activated cell sorting (FACS). HGP-1 showed the moderate affinity when determined with surface plasmon resonance (SPR) technique and high specificity in binding to HGF while assessed by fluorescence-based ELISA assay. The results from MTT and in vitro migration assay indicated that HGF-dependent cell proliferation and migration could be inhibited by HGP-1. In vivo administration of HGP-1 led to an effective inhibitory effect on tumor growth in A549 tumor xenograft models. Moreover, findings from Western Blots revealed that HGP-1 could down-regulated the phosphorylation levels of MET and ERK1/2 initiated by HGF, which suggested that HGP-1 could disrupt the activation of HGF/MET signaling to influence the cell activity. All the data highlighted the potential of HGP-1 to be a potent inhibitor for HGF/MET signaling.
Collapse
Affiliation(s)
- Lisha Chen
- Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China.,Suzhou Institute of Nano-Tech and Nano-Bionics, CAS, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunlin Li
- Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China.,Suzhou Institute of Nano-Tech and Nano-Bionics, CAS, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yimin Zhu
- Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| |
Collapse
|
1041
|
Sánchez-Sanz G, Matallanas D, Nguyen LK, Kholodenko BN, Rosta E, Kolch W, Buchete NV. MST2-RASSF protein-protein interactions through SARAH domains. Brief Bioinform 2015; 17:593-602. [PMID: 26443615 DOI: 10.1093/bib/bbv070] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Indexed: 12/14/2022] Open
Abstract
The detailed, atomistic-level understanding of molecular signaling along the tumor-suppressive Hippo signaling pathway that controls tissue homeostasis by balancing cell proliferation and death through apoptosis is a promising avenue for the discovery of novel anticancer drug targets. The activation of kinases such as Mammalian STE20-Like Protein Kinases 1 and 2 (MST1 and MST2)-modulated through both homo- and heterodimerization (e.g. interactions with Ras association domain family, RASSF, enzymes)-is a key upstream event in this pathway and remains poorly understood. On the other hand, RASSFs (such as RASSF1A or RASSF5) act as important apoptosis activators and tumor suppressors, although their exact regulatory roles are also unclear. We present recent molecular studies of signaling along the Ras-RASSF-MST pathway, which controls growth and apoptosis in eukaryotic cells, including a variety of modern molecular modeling and simulation techniques. Using recently available structural information, we discuss the complex regulatory scenario according to which RASSFs perform dual signaling functions, either preventing or promoting MST2 activation, and thus control cell apoptosis. Here, we focus on recent studies highlighting the special role being played by the specific interactions between the helical Salvador/RASSF/Hippo (SARAH) domains of MST2 and RASSF1a or RASSF5 enzymes. These studies are crucial for integrating atomistic-level mechanistic information about the structures and conformational dynamics of interacting proteins, with information available on their system-level functions in cellular signaling.
Collapse
|
1042
|
Guo J, Erskine P, Coker AR, Gor J, Perkins SJ, Wood SP, Cooper JB. Extension of resolution and oligomerization-state studies of 2,4'-dihydroxyacetophenone dioxygenase from Alcaligenes sp. 4HAP. Acta Crystallogr F Struct Biol Commun 2015; 71:1258-63. [PMID: 26457516 PMCID: PMC4601589 DOI: 10.1107/s2053230x15015873] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 08/25/2015] [Indexed: 11/10/2022] Open
Abstract
The enzyme 2,4'-dihydroxyacetophenone dioxygenase (DAD) catalyses the conversion of 2,4'-dihydroxyacetophenone to 4-hydroxybenzoic acid and formic acid. This enzyme is a very unusual dioxygenase in that it cleaves a C-C bond in a substituent of the aromatic ring rather than within the ring itself. Whilst it has been shown that DAD is a tetramer in solution, the recently solved crystal structure of the Alcaligenes sp. 4HAP enzyme was in fact dimeric rather than tetrameric. Since the use of limited chymotrypsinolysis, which apparently results in removal of the first 20 or so N-terminal residues of DAD, was necessary for crystallization of the protein, it was investigated whether this was responsible for the change in its oligomerization state. Gel-filtration and analytical ultracentrifugation studies were conducted, which confirmed that chymotrypsinolysed DAD has an apparent molecular weight of around 40 kDa, corresponding to a dimer. In contrast, the native enzyme has a molecular weight in the 70-80 kDa region, as expected for the tetramer. The structural basis for tetramerization has been investigated by the use of several docking servers, and the results are remarkably consistent with the tetrameric structure of a homologous cupin protein from Ralstonia eutropha (PDB entry 3ebr).
Collapse
Affiliation(s)
- J. Guo
- Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW2 3PF, England
| | - P. Erskine
- Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW2 3PF, England
| | - A. R. Coker
- Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW2 3PF, England
| | - J. Gor
- Department of Structural and Molecular Biology, Division of Biosciences, University College London, Darwin Building, Gower Street, London WC1E 6BT, England
| | - S. J. Perkins
- Department of Structural and Molecular Biology, Division of Biosciences, University College London, Darwin Building, Gower Street, London WC1E 6BT, England
| | - S. P. Wood
- Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW2 3PF, England
| | - J. B. Cooper
- Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW2 3PF, England
| |
Collapse
|
1043
|
de Vries SJ, Schindler CEM, Chauvot de Beauchêne I, Zacharias M. A web interface for easy flexible protein-protein docking with ATTRACT. Biophys J 2015; 108:462-5. [PMID: 25650913 DOI: 10.1016/j.bpj.2014.12.015] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 12/06/2014] [Accepted: 12/10/2014] [Indexed: 01/03/2023] Open
Abstract
Protein-protein docking programs can give valuable insights into the structure of protein complexes in the absence of an experimental complex structure. Web interfaces can facilitate the use of docking programs by structural biologists. Here, we present an easy web interface for protein-protein docking with the ATTRACT program. While aimed at nonexpert users, the web interface still covers a considerable range of docking applications. The web interface supports systematic rigid-body protein docking with the ATTRACT coarse-grained force field, as well as various kinds of protein flexibility. The execution of a docking protocol takes up to a few hours on a standard desktop computer.
Collapse
Affiliation(s)
- Sjoerd J de Vries
- Physics Department, Technische Universität München, Garching, Germany.
| | | | | | - Martin Zacharias
- Physics Department, Technische Universität München, Garching, Germany
| |
Collapse
|
1044
|
Vreven T, Moal IH, Vangone A, Pierce BG, Kastritis PL, Torchala M, Chaleil R, Jiménez-García B, Bates PA, Fernandez-Recio J, Bonvin AMJJ, Weng Z. Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2. J Mol Biol 2015; 427:3031-41. [PMID: 26231283 PMCID: PMC4677049 DOI: 10.1016/j.jmb.2015.07.016] [Citation(s) in RCA: 248] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 07/17/2015] [Accepted: 07/17/2015] [Indexed: 01/31/2023]
Abstract
We present an updated and integrated version of our widely used protein-protein docking and binding affinity benchmarks. The benchmarks consist of non-redundant, high-quality structures of protein-protein complexes along with the unbound structures of their components. Fifty-five new complexes were added to the docking benchmark, 35 of which have experimentally measured binding affinities. These updated docking and affinity benchmarks now contain 230 and 179 entries, respectively. In particular, the number of antibody-antigen complexes has increased significantly, by 67% and 74% in the docking and affinity benchmarks, respectively. We tested previously developed docking and affinity prediction algorithms on the new cases. Considering only the top 10 docking predictions per benchmark case, a prediction accuracy of 38% is achieved on all 55 cases and up to 50% for the 32 rigid-body cases only. Predicted affinity scores are found to correlate with experimental binding energies up to r=0.52 overall and r=0.72 for the rigid complexes.
Collapse
Affiliation(s)
- Thom Vreven
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Iain H Moal
- Joint BSC-CRG-IRB Research Program in Computational Biology, Life Sciences Department, Barcelona Supercomputing Center, C/Jordi Girona 29, 08034 Barcelona, Spain
| | - Anna Vangone
- Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, 3584CH Utrecht, The Netherlands
| | - Brian G Pierce
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Panagiotis L Kastritis
- Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, 3584CH Utrecht, The Netherlands
| | - Mieczyslaw Torchala
- Biomolecular Modelling Laboratory, The Francis Crick Institute, Lincoln's Inn Fields Laboratory, London WC2A 3LY, United Kingdom
| | - Raphael Chaleil
- Biomolecular Modelling Laboratory, The Francis Crick Institute, Lincoln's Inn Fields Laboratory, London WC2A 3LY, United Kingdom
| | - Brian Jiménez-García
- Joint BSC-CRG-IRB Research Program in Computational Biology, Life Sciences Department, Barcelona Supercomputing Center, C/Jordi Girona 29, 08034 Barcelona, Spain
| | - Paul A Bates
- Biomolecular Modelling Laboratory, The Francis Crick Institute, Lincoln's Inn Fields Laboratory, London WC2A 3LY, United Kingdom.
| | - Juan Fernandez-Recio
- Joint BSC-CRG-IRB Research Program in Computational Biology, Life Sciences Department, Barcelona Supercomputing Center, C/Jordi Girona 29, 08034 Barcelona, Spain.
| | - Alexandre M J J Bonvin
- Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, 3584CH Utrecht, The Netherlands.
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
| |
Collapse
|
1045
|
Amorim AMXP, de Oliveira UC, Faria F, Pasqualoto KFM, Junqueira-de-Azevedo IDLM, Chudzinski-Tavassi AM. Transcripts involved in hemostasis: Exploring salivary complexes from Haementeria vizottoi leeches through transcriptomics, phylogenetic studies and structural features. Toxicon 2015; 106:20-9. [PMID: 26363292 DOI: 10.1016/j.toxicon.2015.09.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 08/27/2015] [Accepted: 09/07/2015] [Indexed: 12/17/2022]
Abstract
Throughout evolution, parasites have adapted in order to successfully intervene in the host defense, producing specific peptides and proteins. Interestingly, these peptides and proteins have been exploited as potential drug candidates against several diseases. Furthermore, biotechnology studies and cDNA libraries have remarkably contributed to identify potentially bioactive molecules. In this regard, herein, a cDNA library of salivary complexes from Haementeria vizottoi leeches was constructed, the transcriptome was characterized and a phylogenetic analysis was performed considering antistasin-like and antiplatelet-like proteins. Hundred twenty three transcripts were identified coding for putative proteins involved in animal feeding (representing about 10% of the expression level). These sequences showed similarities with myohemerythrins, carbonic anhydrases, anticoagulants, antimicrobials, proteases and protease inhibitors. The phylogenetic analysis, regarding antistasin-like and antiplatetlet-like proteins, revealed two main clades in the Rhynchobdellida leeches. As expected, the sequences from H. vizottoi have presented high similarities with those types of proteins. Thus, our findings could be helpful not only to identify new coagulation inhibitors, but also to better understand the biological composition of the salivary complexes.
Collapse
Affiliation(s)
| | | | - Fernanda Faria
- Laboratório de Bioquímica e Biofísica, Instituto Butantan, Av. Vital Brazil, 1500, CEP: 05.503-900, São Paulo, Brazil
| | | | | | - Ana Marisa Chudzinski-Tavassi
- Laboratório de Bioquímica e Biofísica, Instituto Butantan, Av. Vital Brazil, 1500, CEP: 05.503-900, São Paulo, Brazil; Departamento de Bioquímica, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil.
| |
Collapse
|
1046
|
HK022 Nun Requires Arginine-Rich Motif Residues Distinct from λ N. J Bacteriol 2015; 197:3573-82. [PMID: 26350130 DOI: 10.1128/jb.00466-15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 08/24/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Bacteriophage λ N protein binds boxB RNA hairpins in the nut (N utilization) sites of immediate early λ transcripts and interacts with host factors to suppress transcriptional termination at downstream terminators. In opposition to λ N, the Nun protein of HK022 binds the boxBs of coinfecting λ transcripts, interacts with a similar or identical set of host factors, and terminates transcription to suppress λ replication. Comparison of N-boxB and Nun-boxB nuclear magnetic resonance (NMR) structural models suggests similar interactions, though limited mutagenesis of Nun is available. Here, libraries of Nun's arginine-rich motif (ARM) were screened for the ability to exclude λ coinfection, and mutants were assayed for Nun termination with a boxB plasmid reporter system. Several Nun ARM residues appear to be immutable: Asp26, Arg28, Arg29, Arg32, Trp33, and Arg36. Asp26 and Trp33 appear to be unable to contact boxB and are not found at equivalent positions in λ N ARM. To understand if the requirement of Asp26, Trp33, and Arg36 indicated differences between HK022 Nun termination and λ N antitermination complexes, the same Nun libraries were fused to the activation domain of λ N and screened for clones able to complement N-deficient λ. Mutants were assayed for N antitermination. Surprisingly, Asp26 and Trp33 were still essential when Nun ARM was fused to N. Docking suggests that Nun ARM contacts a hydrophobic surface of the NusG carboxy-terminal domain containing residues necessary for Nun function. These findings indicate that Nun ARM relies on distinct contacts in its ternary complex and illustrate how protein-RNA recognition can evolve new regulatory functions. IMPORTANCE λ N protein interacts with host factors to allow λ nut-containing transcripts to elongate past termination signals. A competing bacteriophage, HK022, expresses Nun protein, which causes termination of λ nut transcripts. λ N and HK022 Nun use similar arginine-rich motifs (ARMs) to bind the same boxB RNAs in nut transcripts. Screening libraries of Nun ARM mutants, both in HK022 Nun and in a λ N fusion, revealed amino acids essential to Nun that could bind one or more host factors. Docking suggests that NusG, which is present in both Nun termination and N antitermination, is a plausible partner. These findings could help understand how transcription elongation is regulated and illustrate how subtle differences allow ARMs to evolve new regulatory functions.
Collapse
|
1047
|
Binding interface between the Salmonella σ(S)/RpoS subunit of RNA polymerase and Crl: hints from bacterial species lacking crl. Sci Rep 2015; 5:13564. [PMID: 26338235 PMCID: PMC4559669 DOI: 10.1038/srep13564] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 07/30/2015] [Indexed: 01/30/2023] Open
Abstract
In many Gram-negative bacteria, including Salmonella enterica serovar Typhimurium (S. Typhimurium), the sigma factor RpoS/σS accumulates during stationary phase of growth, and associates with the core RNA polymerase enzyme (E) to promote transcription initiation of genes involved in general stress resistance and starvation survival. Whereas σ factors are usually inactivated upon interaction with anti-σ proteins, σS binding to the Crl protein increases σS activity by favouring its association to E. Taking advantage of evolution of the σS sequence in bacterial species that do not contain a crl gene, like Pseudomonas aeruginosa, we identified and assigned a critical arginine residue in σS to the S. Typhimurium σS-Crl binding interface. We solved the solution structure of S. Typhimurium Crl by NMR and used it for NMR binding assays with σS and to generate in silico models of the σS-Crl complex constrained by mutational analysis. The σS-Crl models suggest that the identified arginine in σS interacts with an aspartate of Crl that is required for σS binding and is located inside a cavity enclosed by flexible loops, which also contribute to the interface. This study provides the basis for further structural investigation of the σS-Crl complex.
Collapse
|
1048
|
Hashmi I, Shehu A. idDock+: Integrating Machine Learning in Probabilistic Search for Protein–Protein Docking. J Comput Biol 2015. [DOI: 10.1089/cmb.2015.0108] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Irina Hashmi
- Department of Computer Science, George Mason University, Fairfax, Virginia
| | - Amarda Shehu
- Department of Computer Science, George Mason University, Fairfax, Virginia
- Department of Bioengineering, George Mason University, Fairfax, Virginia
- School of Systems Biology, George Mason University, Fairfax, Virginia
| |
Collapse
|
1049
|
Guo F, Li SC, Wei Z, Zhu D, Shen C, Wang L. Structural neighboring property for identifying protein-protein binding sites. BMC SYSTEMS BIOLOGY 2015; 9 Suppl 5:S3. [PMID: 26356630 PMCID: PMC4565107 DOI: 10.1186/1752-0509-9-s5-s3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Background The protein-protein interaction plays a key role in the control of many biological functions, such as drug design and functional analysis. Determination of binding sites is widely applied in molecular biology research. Therefore, many efficient methods have been developed for identifying binding sites. In this paper, we calculate structural neighboring property through Voronoi diagram. Using 6,438 complexes, we study local biases of structural neighboring property on interface. Results We propose a novel statistical method to extract interacting residues, and interacting patches can be clustered as predicted interface residues. In addition, structural neighboring property can be adopted to construct a new energy function, for evaluating docking solutions. It includes new statistical property as well as existing energy items. Comparing to existing methods, our approach improves overall Fnat value by at least 3%. On Benchmark v4.0, our method has average Irmsd value of 3.31Å and overall Fnat value of 63%, which improves upon Irmsd of 3.89 Å and Fnat of 49% for ZRANK, and Irmsd of 3.99Å and Fnat of 46% for ClusPro. On the CAPRI targets, our method has average Irmsd value of 3.46 Å and overall Fnat value of 45%, which improves upon Irmsd of 4.18 Å and Fnat of 40% for ZRANK, and Irmsd of 5.12 Å and Fnat of 32% for ClusPro. Conclusions Experiments show that our method achieves better results than some state-of-the-art methods for identifying protein-protein binding sites, with the prediction quality improved in terms of CAPRI evaluation criteria.
Collapse
|
1050
|
Identification of Protein–Protein Interactions by Detecting Correlated Mutation at the Interface. J Chem Inf Model 2015; 55:2042-9. [DOI: 10.1021/acs.jcim.5b00320] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
|