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Detomasi TC, Batka AE, Valastyan JS, Hydorn MA, Craik CS, Bassler BL, Marletta MA. Proteases influence colony aggregation behavior in Vibrio cholerae. J Biol Chem 2023; 299:105386. [PMID: 37898401 PMCID: PMC10709122 DOI: 10.1016/j.jbc.2023.105386] [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: 07/10/2023] [Revised: 10/03/2023] [Accepted: 10/16/2023] [Indexed: 10/30/2023] Open
Abstract
Aggregation behavior provides bacteria protection from harsh environments and threats to survival. Two uncharacterized proteases, LapX and Lap, are important for Vibrio cholerae liquid-based aggregation. Here, we determined that LapX is a serine protease with a preference for cleavage after glutamate and glutamine residues in the P1 position, which processes a physiologically based peptide substrate with a catalytic efficiency of 180 ± 80 M-1s-1. The activity with a LapX substrate identified by a multiplex substrate profiling by mass spectrometry screen was 590 ± 20 M-1s-1. Lap shares high sequence identity with an aminopeptidase (termed VpAP) from Vibrio proteolyticus and contains an inhibitory bacterial prepeptidase C-terminal domain that, when eliminated, increases catalytic efficiency on leucine p-nitroanilide nearly four-fold from 5.4 ± 4.1 × 104 M-1s-1 to 20.3 ± 4.3 × 104 M-1s-1. We demonstrate that LapX processes Lap to its mature form and thus amplifies Lap activity. The increase is approximately eighteen-fold for full-length Lap (95.7 ± 5.6 × 104 M-1s-1) and six-fold for Lap lacking the prepeptidase C-terminal domain (11.3 ± 1.9 × 105 M-1s-1). In addition, substrate profiling reveals preferences for these two proteases that could inform in vivo function. Furthermore, purified LapX and Lap restore the timing of the V. cholerae aggregation program to a mutant lacking the lapX and lap genes. Both proteases must be present to restore WT timing, and thus they appear to act sequentially: LapX acts on Lap, and Lap acts on the substrate involved in aggregation.
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Affiliation(s)
- Tyler C Detomasi
- Department of Chemistry, University of California, Berkeley, Berkeley, California, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
| | - Allison E Batka
- Department of Chemistry, University of California, Berkeley, Berkeley, California, USA
| | - Julie S Valastyan
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA; The Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Molly A Hydorn
- Department of Chemistry, University of California, Berkeley, Berkeley, California, USA; Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
| | - Bonnie L Bassler
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA; The Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Michael A Marletta
- Department of Chemistry, University of California, Berkeley, Berkeley, California, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA.
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2
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Baard V, Bakare OO, Daniel AI, Nkomo M, Gokul A, Keyster M, Klein A. Biocontrol Potential of Bacillus subtilis and Bacillus tequilensis against Four Fusarium Species. Pathogens 2023; 12:pathogens12020254. [PMID: 36839528 PMCID: PMC9962110 DOI: 10.3390/pathogens12020254] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/08/2023] Open
Abstract
The use of biological control agents as opposed to synthetic agrochemicals to control plant pathogens has gained momentum, considering their numerous advantages. The aim of this study is to investigate the biocontrol potential of plant bacterial isolates against Fusarium oxysporum, Fusarium proliferatum, Fusarium culmorum, and Fusarium verticillioides. Isolation, identification, characterization, and in vitro biocontrol antagonistic assays of these isolates against Fusarium species were carried out following standard protocols. The bacterial endophytes were isolated from Glycine max. L leaves (B1), Brassica napus. L seeds (B2), Vigna unguiculata seeds (B3), and Glycine max. L seeds (B4). The bacterial isolates were identified using 16S rRNA PCR sequencing. A phylogenetic analysis shows that the bacterial isolates are closely related to Bacillus subtilis (B1) and Bacillus tequilensis (B2-B4), with an identity score above 98%. All the bacterial isolates produced a significant amount (p < 0.05) of indole acetic acid (IAA), siderophores, and protease activity. In vitro antagonistic assays of these isolates show a significant (p < 0.05) growth inhibition of the fungal mycelia in the following order: F. proliferatum > F. culmorum > F. verticillioides > F. oxysporum, compared to the control. The results suggest that these bacterial isolates are good biocontrol candidates against the selected Fusarium species.
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Affiliation(s)
- Vejonepher Baard
- Plant Omics Laboratory, Department of Biotechnology, University of the Western Cape, Robert Sobukwe Road, Bellville 7530, South Africa
| | - Olalekan Olanrewaju Bakare
- Department of Biochemistry, Faculty of Basic Medical Sciences, Olabisi Onabanjo University, Sagamu 121001, Nigeria
- Environmental Biotechnology Laboratory, Department of Biotechnology, University of the Western Cape, Robert Sobukwe Road, Bellville 7530, South Africa
| | - Augustine Innalegwu Daniel
- Plant Omics Laboratory, Department of Biotechnology, University of the Western Cape, Robert Sobukwe Road, Bellville 7530, South Africa
- Department of Biochemistry, Federal University of Technology, P.M.B 65, Minna 920101, Nigeria
| | - Mbukeni Nkomo
- Department of Agriculture, University of Zululand, Main Road, KwaDlagezwe 3886, South Africa
| | - Arun Gokul
- Department of Plant Sciences, Qwaqwa Campus, University of the Free State, Phuthadithjaba 9866, South Africa
| | - Marshall Keyster
- Environmental Biotechnology Laboratory, Department of Biotechnology, University of the Western Cape, Robert Sobukwe Road, Bellville 7530, South Africa
| | - Ashwil Klein
- Plant Omics Laboratory, Department of Biotechnology, University of the Western Cape, Robert Sobukwe Road, Bellville 7530, South Africa
- Correspondence:
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3
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Roberts MF, Khan HM, Goldstein R, Reuter N, Gershenson A. Search and Subvert: Minimalist Bacterial Phosphatidylinositol-Specific Phospholipase C Enzymes. Chem Rev 2018; 118:8435-8473. [DOI: 10.1021/acs.chemrev.8b00208] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Mary F. Roberts
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | | | - Rebecca Goldstein
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | | | - Anne Gershenson
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
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4
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Hou MH, Chuang CY, Ko TP, Hu NJ, Chou CC, Shih YP, Ho CL, Wang AHJ. Crystal structure of vespid phospholipase A(1) reveals insights into the mechanism for cause of membrane dysfunction. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2016; 68:79-88. [PMID: 26603193 DOI: 10.1016/j.ibmb.2015.11.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 10/27/2015] [Accepted: 11/13/2015] [Indexed: 06/05/2023]
Abstract
Vespid phospholipase A1 (vPLA1) from the black-bellied hornet (Vespa basalis) catalyzes the hydrolysis of emulsified phospholipids and shows potent hemolytic activity that is responsible for its lethal effect. To investigate the mechanism of vPLA1 towards its function such as hemolysis and emulsification, we isolated vPLA1 from V. basalis venom and determined its crystal structure at 2.5 Å resolution. vPLA1 belongs to the α/β hydrolase fold family. It contains a tightly packed β-sheet surrounded by ten α-helices and a Gly-X-Ser-X-Gly motif, characteristic of a serine hydrolyase active site. A bound phospholipid was modeled into the active site adjacent to the catalytic Ser-His-Asp triad indicating that Gln95 is located at hydrogen-bonding distance from the substrate's phosphate group. Moreover, a hydrophobic surface comprised by the side chains of Phe53, Phe62, Met91, Tyr99, Leu197, Ala167 and Pro169 may serve as the acyl chain-binding site. vPLA1 shows global similarity to the N-terminal domain of human pancreatic lipase (HPL), but with some local differences. The lid domain and the β9 loop responsible for substrate selectivity in vPLA1 are shorter than in HPL. Thus, solvent-exposed hydrophilic residues can easily accommodate the polar head groups of phospholipids, thereby accounting for the high activity level of vPLA1. Our result provides a potential explanation for the ability of vPLA1 to hydrolyze phospholipids of cell membrane.
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Affiliation(s)
- Ming-Hon Hou
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 40254, Taiwan; Biotechnology Center, National Chung Hsing University, Taichung 40254, Taiwan.
| | - Chien-Ying Chuang
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 40254, Taiwan
| | - Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Nien-Jen Hu
- Institute of Biochemistry, National Chung Hsing University, Taichung 40254, Taiwan
| | - Chia-Cheng Chou
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Yan-Ping Shih
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Chewn-Lang Ho
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Andrew H-J Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan.
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5
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Özşahin E, Sezen K, Demirbağ Z. Amsacta moorei entomopoxvirus encodes a functional esterase (amv133) with protease activity. Intervirology 2015; 58:41-8. [PMID: 25591507 DOI: 10.1159/000369018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 10/09/2014] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVES Lipolytic genes have been investigated in several viral genomes, and some of them show enzyme activity which can be used for various functions including the production of DNA replication metabolites, rescue from endosomes, and membrane fusion. Amsacta moorei entomopoxvirus (AMEV) replicates in nearly the entire insect body, especially in the adipose tissue. One of the open reading frames (ORFs) in the AMEV genome, amv133, encodes a putative lipase enzyme. In this study, we therefore investigate the enzyme activity of amv133. METHODS amv133 was aligned with known lipase genes and their homologs in entomopoxviruses. Expressed proteins were partially purified and assayed for lipase, esterase and protease. RESULTS We found that amv133 contains all the domains required for a functional lipase enzyme and that it shows a significant similarity with homologs in other entomopoxviruses. Since there is a similarity of the catalytic triad between lipases and serine proteases, we also investigated the protease activity of amv133. Lipase, esterase and protease assays showed that amv133 encodes a functional esterase enzyme with protease activity. CONCLUSION The current data show that amv133 is a conserved gene in all entomopoxvirus genomes sequenced so far and might contribute greatly to degrading the lipids or proteins and hence improve the virus infection.
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Affiliation(s)
- Emine Özşahin
- Department of Biology, Faculty of Science, Karadeniz Technical University, Trabzon, Turkey
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6
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Chakraborty S. DOCLASP - Docking ligands to target proteins using spatial and electrostatic congruence extracted from a known holoenzyme and applying simple geometrical transformations. F1000Res 2014; 3:262. [PMID: 27429737 DOI: 10.12688/f1000research.5145.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/10/2014] [Indexed: 02/04/2023] Open
Abstract
The ability to accurately and effectively predict the interaction between proteins and small drug-like compounds has long intrigued researchers for pedagogic, humanitarian and economic reasons. Protein docking methods (AutoDock, GOLD, DOCK, FlexX and Glide to name a few) rank a large number of possible conformations of protein-ligand complexes using fast algorithms. Previously, it has been shown that structural congruence leading to the same enzymatic function necessitates the congruence of electrostatic properties (CLASP). The current work presents a methodology for docking a ligand into a target protein, provided that there is at least one known holoenzyme with ligand bound - DOCLASP (Docking using CLASP). The contact points of the ligand in the holoenzyme defines a motif, which is used to query the target enzyme using CLASP. If there are significant matches, the holoenzyme and the target protein are superimposed based on congruent atoms. The same linear and rotational transformations are also applied to the ligand, thus creating a unified coordinate framework having the holoenzyme, the ligand and the target enzyme. In the current work, the dipeptidyl peptidase-IV inhibitor vildagliptin was docked to the PI-PLC structure complexed with myo-inositol using DOCLASP. Also, corroboration of the docking of phenylthiourea to the modelled structure of polyphenol oxidase (JrPPO1) from walnut is provided based on the subsequently solved structure of JrPPO1 (PDBid:5CE9). Analysis of the binding of the antitrypanosomial drug suramin to nine non-homologous proteins in the PDB database shows a diverse set of binding motifs, and multiple binding sites in the phospholipase A2-likeproteins from the Bothrops genus of pitvipers. The conformational changes in the suramin molecule on binding highlights the challenges in docking flexible ligands into an already 'plastic' binding site. Thus, DOCLASP presents a method for 'soft docking' ligands to proteins with low computational requirements.
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Affiliation(s)
- Sandeep Chakraborty
- Plant Sciences Department, University of California, Davis, CA, 95616, USA; Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, 400 005, India; Celia Engineers, Navi Mumbai, India
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7
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Chakraborty S. DOCLASP - Docking ligands to target proteins using spatial and electrostatic congruence extracted from a known holoenzyme and applying simple geometrical transformations. F1000Res 2014; 3:262. [PMID: 27429737 PMCID: PMC4934513 DOI: 10.12688/f1000research.5145.3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/14/2016] [Indexed: 12/01/2022] Open
Abstract
The ability to accurately and effectively predict the interaction between proteins and small drug-like compounds has long intrigued researchers for pedagogic, humanitarian and economic reasons. Protein docking methods (AutoDock, GOLD, DOCK, FlexX and Glide to name a few) rank a large number of possible conformations of protein-ligand complexes using fast algorithms. Previously, it has been shown that structural congruence leading to the same enzymatic function necessitates the congruence of electrostatic properties (CLASP). The current work presents a methodology for docking a ligand into a target protein, provided that there is at least one known holoenzyme with ligand bound - DOCLASP (Docking using CLASP). The contact points of the ligand in the holoenzyme defines a motif, which is used to query the target enzyme using CLASP. If there are significant matches, the holoenzyme and the target protein are superimposed based on congruent atoms. The same linear and rotational transformations are also applied to the ligand, thus creating a unified coordinate framework having the holoenzyme, the ligand and the target enzyme. In the current work, the dipeptidyl peptidase-IV inhibitor vildagliptin was docked to the PI-PLC structure complexed with myo-inositol using DOCLASP. Also, corroboration of the docking of phenylthiourea to the modelled structure of polyphenol oxidase (JrPPO1) from walnut is provided based on the subsequently solved structure of JrPPO1 (PDBid:5CE9). Analysis of the binding of the antitrypanosomial drug suramin to nine non-homologous proteins in the PDB database shows a diverse set of binding motifs, and multiple binding sites in the phospholipase A2-likeproteins from the Bothrops genus of pitvipers. The conformational changes in the suramin molecule on binding highlights the challenges in docking flexible ligands into an already ’plastic’ binding site. Thus, DOCLASP presents a method for ’soft docking’ ligands to proteins with low computational requirements.
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Affiliation(s)
- Sandeep Chakraborty
- Plant Sciences Department, University of California, Davis, CA, 95616, USA; Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, 400 005, India; Celia Engineers, Navi Mumbai, India
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8
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Gouran H, Chakraborty S, Rao BJ, Asgeirsson B, Dandekar A. Directed evolution induces tributyrin hydrolysis in a virulence factor of Xylella fastidiosa using a duplicated gene as a template. F1000Res 2014; 3:215. [PMID: 25717364 PMCID: PMC4329599 DOI: 10.12688/f1000research.5147.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/26/2014] [Indexed: 01/22/2023] Open
Abstract
Duplication of genes is one of the preferred ways for natural selection to add advantageous functionality to the genome without having to reinvent the wheel with respect to catalytic efficiency and protein stability. The duplicated secretory virulence factors of Xylella fastidiosa (LesA, LesB and LesC), implicated in Pierce's disease of grape and citrus variegated chlorosis of citrus species, epitomizes the positive selection pressures exerted on advantageous genes in such pathogens. A deeper insight into the evolution of these lipases/esterases is essential to develop resistance mechanisms in transgenic plants. Directed evolution, an attempt to accelerate the evolutionary steps in the laboratory, is inherently simple when targeted for loss of function. A bigger challenge is to specify mutations that endow a new function, such as a lost functionality in a duplicated gene. Previously, we have proposed a method for enumerating candidates for mutations intended to transfer the functionality of one protein into another related protein based on the spatial and electrostatic properties of the active site residues (DECAAF). In the current work, we present in vivo validation of DECAAF by inducing tributyrin hydrolysis in LesB based on the active site similarity to LesA. The structures of these proteins have been modeled using RaptorX based on the closely related LipA protein from Xanthomonas oryzae. These mutations replicate the spatial and electrostatic conformation of LesA in the modeled structure of the mutant LesB as well, providing in silico validation before proceeding to the laborious in vivo work. Such focused mutations allows one to dissect the relevance of the duplicated genes in finer detail as compared to gene knockouts, since they do not interfere with other moonlighting functions, protein expression levels or protein-protein interaction.
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Affiliation(s)
- Hossein Gouran
- Plant Sciences Department, University of California, Davis, CA, 95616, USA
| | - Sandeep Chakraborty
- Plant Sciences Department, University of California, Davis, CA, 95616, USA
- Department of Biological Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai, 400 005, India
| | - Basuthkar J. Rao
- Department of Biological Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai, 400 005, India
| | - Bjarni Asgeirsson
- Science Institute, Department of Biochemistry, University of Iceland, Dunhaga 3, IS-107 Reykjavik, Iceland
| | - Abhaya Dandekar
- Plant Sciences Department, University of California, Davis, CA, 95616, USA
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9
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Chakraborty S. DOCLASP - Docking ligands to target proteins using spatial and electrostatic congruence extracted from a known holoenzyme and applying simple geometrical transformations. F1000Res 2014; 3:262. [PMID: 27429737 DOI: 10.12688/f1000research.5145.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/27/2014] [Indexed: 12/20/2022] Open
Abstract
The ability to accurately and effectively predict the interaction between proteins and small drug-like compounds has long intrigued researchers for pedagogic, humanitarian and economic reasons. Protein docking methods (AutoDock, GOLD, DOCK, FlexX and Glide to name a few) rank a large number of possible conformations of protein-ligand complexes using fast algorithms. Previously, it has been shown that structural congruence leading to the same enzymatic function necessitates the congruence of electrostatic properties (CLASP). The current work presents a methodology for docking a ligand into a target protein, provided that there is at least one known holoenzyme with ligand bound - DOCLASP (Docking using CLASP). The contact points of the ligand in the holoenzyme defines a motif, which is used to query the target enzyme using CLASP. If there are significant matches, the holoenzyme and the target protein are superimposed based on congruent atoms. The same linear and rotational transformations are also applied to the ligand, thus creating a unified coordinate framework having the holoenzyme, the ligand and the target enzyme. In the current work, the dipeptidyl peptidase-IV inhibitor vildagliptin was docked to the PI-PLC structure complexed with myo-inositol using DOCLASP. Also, corroboration of the docking of phenylthiourea to the modelled structure of polyphenol oxidase (JrPPO1) from walnut is provided based on the subsequently solved structure of JrPPO1 (PDBid:5CE9). Analysis of the binding of the antitrypanosomial drug suramin to nine non-homologous proteins in the PDB database shows a diverse set of binding motifs, and multiple binding sites in the phospholipase A2-likeproteins from the Bothrops genus of pitvipers. The conformational changes in the suramin molecule on binding highlights the challenges in docking flexible ligands into an already 'plastic' binding site. Thus, DOCLASP presents a method for 'soft docking' ligands to proteins with low computational requirements.
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Affiliation(s)
- Sandeep Chakraborty
- Plant Sciences Department, University of California, Davis, CA, 95616, USA; Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, 400 005, India; Celia Engineers, Navi Mumbai, India
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10
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Chakraborty S, Rendón-Ramírez A, Ásgeirsson B, Dutta M, Ghosh AS, Oda M, Venkatramani R, Rao BJ, Dandekar AM, Goñi FM. The dipeptidyl peptidase IV inhibitors vildagliptin and K-579 inhibit a phospholipase C: a case of promiscuous scaffolds in proteins. F1000Res 2013. [PMID: 25671081 DOI: 10.12688/f1000research.2-286.v1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The long term side effects of any newly introduced drug is a subject of intense research, and often raging controversies. One such example is the dipeptidyl peptidase-IV (DPP4) inhibitor used for treating type 2 diabetes, which is inconclusively implicated in increased susceptibility to acute pancreatitis. Previously, based on a computational analysis of the spatial and electrostatic properties of active site residues, we have demonstrated that phosphoinositide-specific phospholipase C (PI-PLC) from Bacillus cereus is a prolyl peptidase using in vivo experiments. In the current work, we first report the inhibition of the native activity of PI-PLC by two DPP4 inhibitors - vildagliptin (LAF-237) and K-579. While vildagliptin inhibited PI-PLC at micromolar concentrations, K-579 was a potent inhibitor even at nanomolar concentrations. Subsequently, we queried a comprehensive, non-redundant set of 5000 human proteins (50% similarity cutoff) with known structures using serine protease (SPASE) motifs derived from trypsin and DPP4. A pancreatic lipase and a gastric lipase are among the proteins that are identified as proteins having promiscuous SPASE scaffolds that could interact with DPP4 inhibitors. The presence of such scaffolds in human lipases is expected since they share the same catalytic mechanism with PI-PLC. However our methodology also detects other proteins, often with a completely different enzymatic mechanism, that have significantly congruent domains with the SPASE motifs. The reported elevated levels of serum lipase, although contested, could be rationalized by inhibition of lipases reported here. In an effort to further our understanding of the spatial and electrostatic basis of DPP4 inhibitors, we have also done a comprehensive analysis of all 76 known DPP4 structures liganded to inhibitors till date. Also, the methodology presented here can be easily adopted for other drugs, and provide the first line of filtering in the identification of pathways that might be inadvertently affected due to promiscuous scaffolds in proteins.
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Affiliation(s)
- Sandeep Chakraborty
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, 400 005, India ; Plant Sciences Department, University of California, Davis, CA, 95616, USA
| | | | - Bjarni Ásgeirsson
- Science Institute, Department of Biochemistry, University of Iceland, IS-107 Reykjavik, Iceland
| | - Mouparna Dutta
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
| | - Anindya S Ghosh
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
| | - Masataka Oda
- Division of Microbiology and Infectious Diseases, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8514, Japan
| | - Ravindra Venkatramani
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, 400 005, India
| | - Basuthkar J Rao
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, 400 005, India
| | - Abhaya M Dandekar
- Plant Sciences Department, University of California, Davis, CA, 95616, USA
| | - Félix M Goñi
- Unidad de Bio, Universidad del Pais Vasco, Bilbao, Spain
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11
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Chakraborty S, Rendón-Ramírez A, Ásgeirsson B, Dutta M, Ghosh AS, Oda M, Venkatramani R, Rao BJ, Dandekar AM, Goñi FM. The dipeptidyl peptidase IV inhibitors vildagliptin and K-579 inhibit a phospholipase C: a case of promiscuous scaffolds in proteins. F1000Res 2013; 2:286. [PMID: 25671081 PMCID: PMC4309170 DOI: 10.12688/f1000research.2-286.v3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/29/2015] [Indexed: 12/25/2022] Open
Abstract
The long term side effects of any newly introduced drug is a subject of intense research, and often raging controversies. One such example is the dipeptidyl peptidase-IV (DPP4) inhibitor used for treating type 2 diabetes, which is inconclusively implicated in increased susceptibility to acute pancreatitis. Previously, based on a computational analysis of the spatial and electrostatic properties of active site residues, we have demonstrated that phosphoinositide-specific phospholipase C (PI-PLC) from
Bacillus cereus is a prolyl peptidase using
in vivo experiments. In the current work, we first report the inhibition of the native activity of PI-PLC by two DPP4 inhibitors - vildagliptin (LAF-237) and K-579. While vildagliptin inhibited PI-PLC at micromolar concentrations, K-579 was a potent inhibitor even at nanomolar concentrations. Subsequently, we queried a comprehensive, non-redundant set of 5000 human proteins (50% similarity cutoff) with known structures using serine protease (SPASE) motifs derived from trypsin and DPP4. A pancreatic lipase and a gastric lipase are among the proteins that are identified as proteins having promiscuous SPASE scaffolds that could interact with DPP4 inhibitors. The presence of such scaffolds in human lipases is expected since they share the same catalytic mechanism with PI-PLC. However our methodology also detects other proteins, often with a completely different enzymatic mechanism, that have significantly congruent domains with the SPASE motifs. The reported elevated levels of serum lipase, although contested, could be rationalized by inhibition of lipases reported here. In an effort to further our understanding of the spatial and electrostatic basis of DPP4 inhibitors, we have also done a comprehensive analysis of all 76 known DPP4 structures liganded to inhibitors till date. Also, the methodology presented here can be easily adopted for other drugs, and provide the first line of filtering in the identification of pathways that might be inadvertently affected due to promiscuous scaffolds in proteins.
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Affiliation(s)
- Sandeep Chakraborty
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, 400 005, India ; Plant Sciences Department, University of California, Davis, CA, 95616, USA
| | | | - Bjarni Ásgeirsson
- Science Institute, Department of Biochemistry, University of Iceland, IS-107 Reykjavik, Iceland
| | - Mouparna Dutta
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
| | - Anindya S Ghosh
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
| | - Masataka Oda
- Division of Microbiology and Infectious Diseases, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8514, Japan
| | - Ravindra Venkatramani
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, 400 005, India
| | - Basuthkar J Rao
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, 400 005, India
| | - Abhaya M Dandekar
- Plant Sciences Department, University of California, Davis, CA, 95616, USA
| | - Félix M Goñi
- Unidad de Bio, Universidad del Pais Vasco, Bilbao, Spain
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12
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Chakraborty S, Venkatramani R, Rao BJ, Asgeirsson B, Dandekar AM. The electrostatic profile of consecutive Cβ atoms applied to protein structure quality assessment. F1000Res 2013; 2:243. [PMID: 25506420 PMCID: PMC4257144 DOI: 10.12688/f1000research.2-243.v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/16/2014] [Indexed: 02/10/2024] Open
Abstract
The structure of a protein provides insight into its physiological interactions with other components of the cellular soup. Methods that predict putative structures from sequences typically yield multiple, closely-ranked possibilities. A critical component in the process is the model quality assessing program (MQAP), which selects the best candidate from this pool of structures. Here, we present a novel MQAP based on the physical properties of sidechain atoms. We propose a method for assessing the quality of protein structures based on the electrostatic potential difference (EPD) of Cβ atoms in consecutive residues. We demonstrate that the EPDs of Cβ atoms on consecutive residues provide unique signatures of the amino acid types. The EPD of Cβ atoms are learnt from a set of 1000 non-homologous protein structures with a resolution cuto of 1.6 Å obtained from the PISCES database. Based on the Boltzmann hypothesis that lower energy conformations are proportionately sampled more, and on Annsen's thermodynamic hypothesis that the native structure of a protein is the minimum free energy state, we hypothesize that the deviation of observed EPD values from the mean values obtained in the learning phase is minimized in the native structure. We achieved an average specificity of 0.91, 0.94 and 0.93 on hg_structal, 4state_reduced and ig_structal decoy sets, respectively, taken from the Decoys `R' Us database. The source code and manual is made available at https://github.com/sanchak/mqap and permanently available on 10.5281/zenodo.7134.
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Affiliation(s)
- Sandeep Chakraborty
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, 400 005, India
| | - Ravindra Venkatramani
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, 400 005, India
| | - Basuthkar J. Rao
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, 400 005, India
| | - Bjarni Asgeirsson
- Science Institute, Department of Biochemistry, University of Iceland, IS-107 Reykjavik, Iceland
| | - Abhaya M. Dandekar
- Plant Sciences Department, University of California,, Davis, CA, 95616, USA
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13
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Chakraborty S, Venkatramani R, Rao BJ, Asgeirsson B, Dandekar AM. Protein structure quality assessment based on the distance profiles of consecutive backbone Cα atoms. F1000Res 2013; 2:211. [PMID: 24555103 DOI: 10.12688/f1000research.2-211.v1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/10/2013] [Indexed: 01/22/2023] Open
Abstract
Predicting the three dimensional native state structure of a protein from its primary sequence is an unsolved grand challenge in molecular biology. Two main computational approaches have evolved to obtain the structure from the protein sequence - ab initio/de novo methods and template-based modeling - both of which typically generate multiple possible native state structures. Model quality assessment programs (MQAP) validate these predicted structures in order to identify the correct native state structure. Here, we propose a MQAP for assessing the quality of protein structures based on the distances of consecutive Cα atoms. We hypothesize that the root-mean-square deviation of the distance of consecutive Cα (RDCC) atoms from the ideal value of 3.8 Å, derived from a statistical analysis of high quality protein structures (top100H database), is minimized in native structures. Based on tests with the top100H set, we propose a RDCC cutoff value of 0.012 Å, above which a structure can be filtered out as a non-native structure. We applied the RDCC discriminator on decoy sets from the Decoys 'R' Us database to show that the native structures in all decoy sets tested have RDCC below the 0.012 Å cutoff. While most decoy sets were either indistinguishable using this discriminator or had very few violations, all the decoy structures in the fisa decoy set were discriminated by applying the RDCC criterion. This highlights the physical non-viability of the fisa decoy set, and possible issues in benchmarking other methods using this set. The source code and manual is made available at https://github.com/sanchak/mqap and permanently available on 10.5281/zenodo.7134.
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Affiliation(s)
- Sandeep Chakraborty
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, 400 005, India
| | - Ravindra Venkatramani
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, 400 005, India
| | - Basuthkar J Rao
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, 400 005, India
| | - Bjarni Asgeirsson
- Science Institute, Department of Biochemistry, University of Iceland, Reykjavik, IS-107, Iceland
| | - Abhaya M Dandekar
- Plant Sciences Department, University of California, Davis, CA 95616, USA
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14
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Chakraborty S, Venkatramani R, Rao BJ, Asgeirsson B, Dandekar AM. The electrostatic profile of consecutive Cβ atoms applied to protein structure quality assessment. F1000Res 2013; 2:243. [PMID: 25506420 PMCID: PMC4257144 DOI: 10.12688/f1000research.2-243.v3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/16/2014] [Indexed: 12/23/2022] Open
Abstract
The structure of a protein provides insight into its physiological interactions with other components of the cellular soup. Methods that predict putative structures from sequences typically yield multiple, closely-ranked possibilities. A critical component in the process is the model quality assessing program (MQAP), which selects the best candidate from this pool of structures. Here, we present a novel MQAP based on the physical properties of sidechain atoms. We propose a method for assessing the quality of protein structures based on the electrostatic potential difference (EPD) of Cβ atoms in consecutive residues. We demonstrate that the EPDs of Cβ atoms on consecutive residues provide unique signatures of the amino acid types. The EPD of Cβ atoms are learnt from a set of 1000 non-homologous protein structures with a resolution cuto of 1.6 Å obtained from the PISCES database. Based on the Boltzmann hypothesis that lower energy conformations are proportionately sampled more, and on Annsen's thermodynamic hypothesis that the native structure of a protein is the minimum free energy state, we hypothesize that the deviation of observed EPD values from the mean values obtained in the learning phase is minimized in the native structure. We achieved an average specificity of 0.91, 0.94 and 0.93 on hg_structal, 4state_reduced and ig_structal decoy sets, respectively, taken from the Decoys `R' Us database. The source code and manual is made available at
https://github.com/sanchak/mqap and permanently available on 10.5281/zenodo.7134.
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Affiliation(s)
- Sandeep Chakraborty
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, 400 005, India
| | - Ravindra Venkatramani
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, 400 005, India
| | - Basuthkar J Rao
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, 400 005, India
| | - Bjarni Asgeirsson
- Science Institute, Department of Biochemistry, University of Iceland, IS-107 Reykjavik, Iceland
| | - Abhaya M Dandekar
- Plant Sciences Department, University of California,, Davis, CA, 95616, USA
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