1
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Tanwar N, Ojha R, Aggarwal S, Prajapati VK, Munde M. Design of inhibitor peptide sequences based on the interfacial knowledge of the protein G-IgG crystallographic complex and their binding studies with IgG. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2024; 53:159-170. [PMID: 38493432 DOI: 10.1007/s00249-024-01704-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/18/2024] [Accepted: 03/06/2024] [Indexed: 03/19/2024]
Abstract
Protein-protein interactions (PPI) have emerged as valuable targets in medicinal chemistry due to their key roles in important biological processes. The modulation of PPI by small peptides offers an excellent opportunity to develop drugs against human diseases. Here, we exploited the knowledge of the binding interface of the IgG-protein G complex (PDB:1FCC) for designing peptides that can inhibit these complexes. Herein, we have designed several closely related peptides, and the comparison of results from experiments and computational studies indicated that all the peptides bind close to the expected binding site on IgG and the complexes are stable. A minimal sequence consisting of 11 amino acids (P5) with binding constants in the range of 100 nM was identified. We propose that the main affinity differences across the series of peptides arose from the presence of polar amino acid residues. Further, the molecular dynamic studies helped to understand the dynamic properties of complexes in terms of flexibility of residues and structural stability at the interface. The ability of P5 to compete with the protein G in recognizing IgG can help in the detection and purification of antibodies. Further, it can serve as a versatile tool for a better understanding of protein-protein interactions.
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Affiliation(s)
- Neetu Tanwar
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Rupal Ojha
- Department of Nephrology, Washington University School of Medicine, St. Louis, MO, USA
| | - Soumya Aggarwal
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | | | - Manoj Munde
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
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2
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Liu G, An H, Tang L, Chi Z, Bi Y, Ye Z, Zhao H, Xiang L, Feng N, Mo C, Xu D. Activated DBP degradation and relevant signal transduction path via quorum sensing autoinducers in Streptomyces sp. SH5. JOURNAL OF HAZARDOUS MATERIALS 2024; 466:133571. [PMID: 38266588 DOI: 10.1016/j.jhazmat.2024.133571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 12/07/2023] [Accepted: 01/17/2024] [Indexed: 01/26/2024]
Abstract
Microbe-mediated DBP (dibutyl phthalate) mineralization is acknowledged to be affected by diverse extracellular factors. However, little is known about the regulatory effects from quorum sensing (QS) signals. In this study, extracellularly applied QS signals A-like (hydroxymethyl dihydrofuran) was discovered to significantly enhance DBP degradation efficiency in Streptomyces sp. SH5. Monobutyl phthalate, protocatechuic acid and beta-ketoadipate were discovered as degradation intermediates by HPLC-TOF-MS/MS. Multi-omics analysis revealed the up-regulation of multiple hydrolases, transferases and decarboxylases that potentially contributed to A-like accelerated DBP degradation. Transcription of Orf2708, an orthologue of global transcriptional activator, was significantly induced by A-like. Orf2708 was demonstrated to interact specifically with the promoter of hydrolase orf2879 gene by EMSA, and the overexpression of orf2879 led to an enhanced DBP degradation in SH5. Taken together with the molecular docking studies showing the stability of ligand-receptor complex of A-like and its potential receptor Orf3712, a hierarchical regulatory cascade underlying the QS signal mediated DBP degradation was proposed as A-like/Orf3712 duplex formation, enhanced orf2708 expression and the downstream specific activation of hydrolase Orf2879. Our study presents the first evidence of GBLs-type promoted DBP degradation among bacteria, and the elucidated signal transduction path indicates a universal application potential of this activation strategy.
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Affiliation(s)
- Ganxing Liu
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou 510632, PR China
| | - Hao An
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou 510632, PR China
| | - Lei Tang
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou 510632, PR China
| | - Zhewei Chi
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou 510632, PR China
| | - Yunwen Bi
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou 510632, PR China
| | - Zeqi Ye
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou 510632, PR China
| | - Haiming Zhao
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou 510632, PR China
| | - Lei Xiang
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou 510632, PR China
| | - Naixian Feng
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou 510632, PR China.
| | - Cehui Mo
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou 510632, PR China.
| | - Delin Xu
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou 510632, PR China.
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3
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Gupta S, Tiwari N, Verma J, Waseem M, Subbarao N, Munde M. Estimation of a stronger heparin binding locus in fibronectin domain III14using thermodynamics and molecular dynamics. RSC Adv 2020; 10:20288-20301. [PMID: 35520402 PMCID: PMC9054198 DOI: 10.1039/d0ra01773f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/19/2020] [Indexed: 01/04/2023] Open
Abstract
The HEP II (Heparin-binding site II) region of fibronectin (FN) containing domain III14 plays a crucial role in cell adhesion and migration through heparin-binding on the cell surface. There are two such fibronectin heparin interacting peptide (FHIP I and FHIP II) sequences present in HEP II. However, the molecular principles by which these sites orchestrate heparin-binding processes are poorly understood. Such knowledge would have great implications in the therapeutic targeting of FN. With this aim, we have explored the binding studies of FHIP I and FHIP II with heparin using various biophysical methods. A fluorescence melting study specifically revealed the preference of heparin for domain III in FN, indicating the key contribution of FHIP I and FHIP II in heparin binding. In isothermal titration calorimetry (ITC), the higher binding affinity observed for FHIP II (∼107 mol−1) compared to FHIP I (∼106 mol−1) is expected due to the presence of a superior cluster of Arg and Lys residues in FHIP II, which can facilitate specific H-bonding interactions with heparin. Based on heat capacity changes, the key role of H-bonding, electrostatic and hydrophobic interactions was demonstrated in binding. Finally, the molecular docking and MD simulation results reinforced that the interaction of heparin (dodecasaccharide) is stronger and stable with the FHIP II peptide. The results described here suggest that these peptides provide all the structural and thermodynamic elements necessary for heparin-binding of HEP II of FN. Subsequently, it can be concluded that FHIP II could be a better location for therapeutic intervention in cell adhesion activity by FN. Binding Thermodynamics of FHIP I and FHIP II with heparin.![]()
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Affiliation(s)
- Sakshi Gupta
- School of Physical Sciences
- Jawaharlal Nehru University
- New Delhi-110067
- India
| | - Neha Tiwari
- School of Physical Sciences
- Jawaharlal Nehru University
- New Delhi-110067
- India
| | - Jyoti Verma
- School of Computational and Integrative Sciences
- Jawaharlal Nehru University
- New Delhi-110067
- India
| | - Mohd Waseem
- School of Computational and Integrative Sciences
- Jawaharlal Nehru University
- New Delhi-110067
- India
| | - Naidu Subbarao
- School of Computational and Integrative Sciences
- Jawaharlal Nehru University
- New Delhi-110067
- India
| | - Manoj Munde
- School of Physical Sciences
- Jawaharlal Nehru University
- New Delhi-110067
- India
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4
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Gandhi S, Roy I. Synthesis and characterization of manganese ferrite nanoparticles, and its interaction with bovine serum albumin: A spectroscopic and molecular docking approach. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111871] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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5
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Xu G, Yang S. Regulatory and evolutionary roles of pseudo γ-butyrolactone receptors in antibiotic biosynthesis and resistance. Appl Microbiol Biotechnol 2019; 103:9373-9378. [PMID: 31728585 DOI: 10.1007/s00253-019-10219-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 10/16/2019] [Accepted: 10/22/2019] [Indexed: 01/30/2023]
Abstract
Bacteria modulate their physiological behavior by responding to various signal molecules. The signals are received by cognate receptors, which usually mediate transcriptional regulation. Streptomyces employ γ-butyrolactones (GBLs) and cognate GBL receptors (GblRs) to regulate secondary metabolism and morphological development. However, there are additional transcriptional regulators called pseudo GblR regulators, which cannot bind GBLs and are not directly associated with GBL synthase. The pseudo GblR regulators may act as transcriptional repressors and respond to antibiotic signals. They play regulatory roles in coordination of antibiotic biosynthesis by connecting the hormone feed-forward loops and the antibiotic feedback loops. As the TetR family members, they might also have evolutionary roles between the transcriptional regulators of quorum sensing and antibiotic resistance. Understanding the regulatory and evolutionary roles of the pseudo GblR family would be helpful for fine-tuning regulation of antibiotic biosynthesis and resistance.
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Affiliation(s)
- Gangming Xu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
| | - Suiqun Yang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
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6
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Banerjee S, Selim M, Saha A, Mukherjea KK. Radiation induced DNA damage and its protection by a gadolinium(III) complex: Spectroscopic, molecular docking and gel electrophoretic studies. Int J Biol Macromol 2019; 127:520-528. [PMID: 30633933 DOI: 10.1016/j.ijbiomac.2019.01.031] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 12/21/2018] [Accepted: 01/07/2019] [Indexed: 12/24/2022]
Abstract
The current work describes the efficacy of an artificially synthesized Gd(III) complex as a potential radioprotecting molecule. The work involves utilization of spectroscopic and electrophoretic techniques to investigate the radioprotecting behavior of the Gd(III) complex. Spectroscopic studies revealed that the complex interacted strongly with DNA while molecular docking studies suggested groove binding through H-bond formation and other non-covalent interactions. The Gd(III) complex was found to impart 94% and 91% protection to irradiatively damaged DNA at radiation doses of 20 and 25 Gy respectively. The protection is believed to occur via radical scavenging mechanism and the antioxidant behavior of the complex suggested a strong radical scavenging property.
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Affiliation(s)
| | - Md Selim
- Department of Chemistry, Vivekananda College, Thakurpukur, Kolkata 700063, India
| | - Abhijit Saha
- UGC-DAE-CSR, Kolkata Centre, Bidhannagar, Kolkata 700098, India
| | - Kalyan K Mukherjea
- Department of Chemistry, Jadavpur University, Kolkata 700032, India; Department of Chemistry, Aliah University, Newtown, Kolkata 700160, India.
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7
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Sarkale AM, Kumar A, Appayee C. Organocatalytic Approach for Short Asymmetric Synthesis of (R)-Paraconyl Alcohol: Application to the Total Syntheses of IM-2, SCB2, and A-Factor γ-Butyrolactone Autoregulators. J Org Chem 2018; 83:4167-4172. [DOI: 10.1021/acs.joc.8b00122] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Abhijeet M. Sarkale
- Discipline of Chemistry, Indian Institute of Technology Gandhinagar,
Palaj, Gandhinagar, Gujarat 382355, India
| | - Amit Kumar
- Discipline of Chemistry, Indian Institute of Technology Gandhinagar,
Palaj, Gandhinagar, Gujarat 382355, India
| | - Chandrakumar Appayee
- Discipline of Chemistry, Indian Institute of Technology Gandhinagar,
Palaj, Gandhinagar, Gujarat 382355, India
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8
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Mariam J, Anand R. Fluorescence Quenching Studies of γ-Butyrolactone-Binding Protein (CprB) from Streptomyces coelicolor A3(2). Methods Mol Biol 2018; 1673:131-143. [PMID: 29130170 DOI: 10.1007/978-1-4939-7309-5_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Fluorescence spectroscopy is an important analytical tool which is widely employed to study biological systems. This technique can be applied to qualitatively and quantitatively probe protein-ligand interactions primarily because of its sensitivity, selectivity, nondestructive and rapid form of analysis. In this chapter we describe the utility of this technique to establish a label-free, universal screening protocol for putative γ-butyrolactone (GBL) receptors by exploiting the intrinsic fluorescence of a highly conserved tryptophan residue that constitutes the hydrophobic pocket for GBL binding, a unique feature possessed by this family of receptors. Here we demonstrate this technique using a combination of steady-state fluorescence quenching methods and fluorescence lifetime decay kinetics using CprB protein from Streptomyces coelicolor A3(2) as a model system. Interaction data between CprB and two chemically synthesized GBLs involved in quorum sensing, Cp1 and Cp2, have been used as example.
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Affiliation(s)
- Jessy Mariam
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, Maharashtra, 400076, India
| | - Ruchi Anand
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, Maharashtra, 400076, India.
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9
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Tinklepaugh J, Smith BM, Hanlon E, Zubieta C, Bou-Abdallah F, Doyle RP. Exploring the Multiligand Binding Specificity of Saposin B Reveals Two Binding Sites. ACS OMEGA 2017; 2:7141-7145. [PMID: 29104953 PMCID: PMC5664142 DOI: 10.1021/acsomega.7b01334] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 10/11/2017] [Indexed: 06/07/2023]
Abstract
Saposin B (SapB) is a human lysosomal protein, critical for the degradation of O-sulfogalactosylceramide (sulfatide). SapB binds sulfatide and presents it to the active site of the enzyme arylsulfatase A. Deficiency of SapB leads to fatal activator-deficient metachromatic leukodystrophy. Given the conformational flexibility and the large hydrophobic "pocket" produced upon (physiologically relevant) homodimerization, SapB may have broader substrate diversity than originally thought. Herein, we present evidence using fluorescence spectroscopy and computational docking studies that SapB binds a wide variety of ligands at KD values varying from micromolar to nanomolar, with entropy being the primary driving force. We further demonstrate, for the first time, that SapB has two binding sites that can sequentially (and in a preferred order) accommodate up to two ligands at once.
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Affiliation(s)
- Jay Tinklepaugh
- Department
of Chemistry, Syracuse University, 111 College Place, Syracuse, New York 13244, United States
| | - Britannia M. Smith
- Department
of Chemistry, State University of New York
at Potsdam, Potsdam, New York 13676, United
States
| | - Etta Hanlon
- Department
of Chemistry, Syracuse University, 111 College Place, Syracuse, New York 13244, United States
| | - Chloe Zubieta
- Laboratoire
de Physiologie Cellulaire & Végétale, iRTSV, UMR 5168, CNRS/CEA/INRA/Univ. Grenoble Alpes, Grenoble 38054, France
| | - Fadi Bou-Abdallah
- Department
of Chemistry, State University of New York
at Potsdam, Potsdam, New York 13676, United
States
| | - Robert P. Doyle
- Department
of Chemistry, Syracuse University, 111 College Place, Syracuse, New York 13244, United States
- Department
of Medicine, State University of New York
at Upstate Medical University, Syracuse, New York 13210, United States
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10
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Mansouri A, Mousavi M, Attar F, Saboury AA, Falahati M. Interaction of manganese nanoparticle with cytochrome c: A multi-spectroscopic study. Int J Biol Macromol 2017; 106:78-86. [PMID: 28818722 DOI: 10.1016/j.ijbiomac.2017.07.175] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 07/25/2017] [Accepted: 07/30/2017] [Indexed: 12/19/2022]
Abstract
In this paper, the conformational changes of cytochrome c (cyt c) upon interaction with manganese nanoparticle (Mn-NP) were examined using dynamic light scattering (DLS), transmission electron microscopy (TEM), Fourier transform infrared spectroscopy (FTIR), zeta potential, fluorescence spectroscopy, and circular dichroism (CD) spectroscopy methods. DLS and TEM analysis exhibited the structure of Mn-NP was less than 50nm. FTIR bands were similar to those reported for Mn-NP. Zeta potential measurements showed positive charge distribution for Mn-NP (4.71±0.71mV) at pH 7.8. It was revealed that the mechanism of fluorescence quenching incorporated both dynamic and static quenching. Also, binding site and binding constant increased as the temperature is raised. The positive sign of ΔH° and ΔS° suggested that hydrophobic forces are indicative forces in the interaction between cyt c and Mn-NP. Synchronous fluorescence spectra revealed that the conformation of protein was not perturbed around tryptophan (Trp) and tyrosine (Tyr) residues. CD analysis suggested that there was a conformational change at tertiary structure levels of cyt c in the vicinity of phenylalanine (Phe) residues, while the secondary structure of protein was not altered. This study facilitates a deeper insight on the interaction mechanisms between NPs and biological macromolecules.
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Affiliation(s)
- Anali Mansouri
- Department of Cell and Molecular Biology, Faculty of Advance Science and Technology, Pharmaceutical Sciences Branch, Islamic Azad University (IAUPS), Tehran, Iran
| | - Mina Mousavi
- Department of Cell and Molecular Biology, Faculty of Advance Science and Technology, Pharmaceutical Sciences Branch, Islamic Azad University (IAUPS), Tehran, Iran
| | - Farnoosh Attar
- Department of Biology, Faculty of Food Industry & Agriculture, Standard Research Institute (SRI), Karaj, Iran
| | - Ali Akbar Saboury
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Mojtaba Falahati
- Department of Nanotechnology, Faculty of Advance Science and Technology, Pharmaceutical Sciences Branch, Islamic Azad University (IAUPS), Tehran, Iran.
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11
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Ray S, Maitra A, Biswas A, Panjikar S, Mondal J, Anand R. Functional insights into the mode of DNA and ligand binding of the TetR family regulator TylP from Streptomyces fradiae. J Biol Chem 2017; 292:15301-15311. [PMID: 28739805 DOI: 10.1074/jbc.m117.788000] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 07/21/2017] [Indexed: 01/18/2023] Open
Abstract
Tetracycline repressors (TetRs) modulate multidrug efflux pathways in several pathogenic bacteria. In Streptomyces, they additionally regulate secondary metabolic pathways like antibiotic production. For instance, in the antibiotic producer Streptomyces fradiae, a layered network of TetRs regulates the levels of the commercially important antibiotic tylosin, with TylP occupying the top of this cascading network. TetRs exist in two functional states, the DNA-bound and the ligand-bound form, which are allosterically regulated. Here, to develop deeper insights into the factors that govern allostery, the crystal structure of TylP was solved to a resolution of 2.3 Å. The structure revealed that TylP possesses several unique features; notably, it harbors a unique C-terminal helix-loop extension that spans the entire length of the structure. This anchor connects the DNA-binding domain (DBD) with the ligand-binding domain (LBD) via a mix of positively charged and hydrogen-bonding interactions. Supporting EMSA studies with a series of ΔC truncated versions show that a systematic deletion of this region results in complete loss of DNA binding. The structure additionally revealed that TylP is markedly different in the orientation of its DBD and LBD architecture and the dimeric geometry from its hypothesized Streptomyces homologue CprB, which is a γ-butyrolactone regulator. Rather, TylP is closer in structural design to macrolide-binding TetRs found in pathogens. Supporting molecular dynamic studies suggested that TylP binds a macrolide intermediate in the tylosin pathway. Collectively, the structure along with corroborating biochemical studies provided insights into the novel mode of regulation of TetRs in antibiotic-producing organisms.
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Affiliation(s)
- Shamayeeta Ray
- From the Department of Chemistry, Indian Institute of Technology Bombay, Mumbai-400076, India.,the IITB-Monash Research Academy, Mumbai-400076, India
| | - Anwesha Maitra
- From the Department of Chemistry, Indian Institute of Technology Bombay, Mumbai-400076, India
| | - Anwesha Biswas
- From the Department of Chemistry, Indian Institute of Technology Bombay, Mumbai-400076, India
| | - Santosh Panjikar
- the Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia.,the Australian Synchrotron, Victoria 3168, Australia, and
| | - Jagannath Mondal
- the Tata Institute of Fundamental Research (TIFR) Centre for Interdisciplinary Sciences, Hyderabad-500075, India
| | - Ruchi Anand
- From the Department of Chemistry, Indian Institute of Technology Bombay, Mumbai-400076, India,
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12
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13
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Volatile Organic Compound Gamma-Butyrolactone Released upon Herpes Simplex Virus Type -1 Acute Infection Modulated Membrane Potential and Repressed Viral Infection in Human Neuron-Like Cells. PLoS One 2016; 11:e0161119. [PMID: 27537375 PMCID: PMC4990300 DOI: 10.1371/journal.pone.0161119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 07/29/2016] [Indexed: 12/14/2022] Open
Abstract
Herpes Simplex Virus Type -1 (HSV-1) infections can cause serious complications such as keratitis and encephalitis. The goal of this study was to identify any changes in the concentrations of volatile organic compounds (VOCs) produced during HSV-1 infection of epithelial cells that could potentially be used as an indicator of a response to stress. An additional objective was to study if any VOCs released from acute epithelial infection may influence subsequent neuronal infection to facilitate latency. To investigate these hypotheses, Vero cells were infected with HSV-1 and the emission of VOCs was analyzed using two-dimensional gas chromatograph/mass spectrometry (2D GC/MS). It was observed that the concentrations of gamma-butyrolactone (GBL) in particular changed significantly after a 24-hour infection. Since HSV-1 may establish latency in neurons after the acute infection, GBL was tested to determine if it exerts neuronal regulation of infection. The results indicated that GBL altered the resting membrane potential of differentiated LNCaP cells and promoted a non-permissive state of HSV-1 infection by repressing viral replication. These observations may provide useful clues towards understanding the complex signaling pathways that occur during the HSV-1 primary infection and establishment of viral latency.
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14
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Niu G, Chater KF, Tian Y, Zhang J, Tan H. Specialised metabolites regulating antibiotic biosynthesis in Streptomyces spp. FEMS Microbiol Rev 2016; 40:554-73. [PMID: 27288284 DOI: 10.1093/femsre/fuw012] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2016] [Indexed: 12/11/2022] Open
Abstract
Streptomyces bacteria are the major source of antibiotics and other secondary metabolites. Various environmental and physiological conditions affect the onset and level of production of each antibiotic by influencing concentrations of the ligands for conserved global regulatory proteins. In addition, as reviewed here, well-known autoregulators such as γ-butyrolactones, themselves products of secondary metabolism, accumulate late in growth to concentrations allowing their effective interaction with cognate binding proteins, in a necessary prelude to antibiotic biosynthesis. Most autoregulator binding proteins target the conserved global regulatory gene adpA, and/or regulatory genes for 'cluster-situated regulators' (CSRs) linked to antibiotic biosynthetic gene clusters. It now appears that some CSRs bind intermediates and end products of antibiotic biosynthesis, with regulatory effects interwoven with those of autoregulators. These ligands can exert cross-pathway effects within producers of more than one antibiotic, and when excreted into the extracellular environment may have population-wide effects on production, and mediate interactions with neighbouring microorganisms in natural communities, influencing speciation. Greater understanding of these autoregulatory and cross-regulatory activities may aid the discovery of new signalling molecules and their use in activating cryptic antibiotic biosynthetic pathways.
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Affiliation(s)
- Guoqing Niu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Keith F Chater
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Yuqing Tian
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jihui Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Huarong Tan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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15
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Prasanth S, Raj DR, Thomas RK, Vineeshkumar TV, Sudarsanakumar C. A systematic investigation on the interaction of l-cysteine functionalised Mn3O4 nanoparticles with lysozyme. RSC Adv 2016. [DOI: 10.1039/c6ra20714f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Interactions of cysteine capped Mn3O4 nanoparticles with HEWL.
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Affiliation(s)
- S. Prasanth
- School of Pure and Applied Physics
- Mahatma Gandhi University Kottayam
- Kerala
- India 686560
| | - D. Rithesh Raj
- School of Pure and Applied Physics
- Mahatma Gandhi University Kottayam
- Kerala
- India 686560
| | - Riju K. Thomas
- School of Pure and Applied Physics
- Mahatma Gandhi University Kottayam
- Kerala
- India 686560
| | - T. V. Vineeshkumar
- School of Pure and Applied Physics
- Mahatma Gandhi University Kottayam
- Kerala
- India 686560
| | - C. Sudarsanakumar
- School of Pure and Applied Physics
- Mahatma Gandhi University Kottayam
- Kerala
- India 686560
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16
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Biswas A, Narayan S, Kallianpur MV, Krishnamoorthy G, Anand R. Mode of DNA binding with γ-butyrolactone receptor protein CprB from Streptomyces coelicolor revealed by site-specific fluorescence dynamics. Biochim Biophys Acta Gen Subj 2015; 1850:2283-92. [PMID: 26278022 DOI: 10.1016/j.bbagen.2015.08.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 07/16/2015] [Accepted: 08/12/2015] [Indexed: 11/27/2022]
Abstract
BACKGROUND The γ-butyrolactone (GBL) binding transcription factors in Streptomyces species are known for their involvement in quorum sensing where they control the expression of various genes initiating secondary metabolic pathways. The structurally characterized member of this family CprB from Streptomyces coelicolor had earlier been demonstrated to bind a multitude of sequences containing a specific binding signature. Though structural breakthrough has been obtained for its complex with a consensus DNA sequence there is, however a dearth of information regarding the overall and site specific dynamics of protein-DNA interaction. METHODS To delineate the effect of CprB on the bound DNA, changes in motional dynamics of the fluorescent probe 2-aminopurine were monitored at three conserved base positions (5th, 12th and 23rd) for two DNA sequences: the consensus and the biologically relevant cognate element, on complex formation. RESULTS The changes in lifetime and generalized order parameter revealed a similarity in the binding pattern of the protein to both sequences with greater dynamic restriction at the end positions, 5th and 23rd, as compared to the middle 12th position. Also differences within this pattern demonstrated the influence of even small changes in sequence on protein interactions. CONCLUSIONS Here the study of motional dynamics was instrumental in establishing a structural footprint for the cognate DNA sequence and explaining the dynamics for the consensus DNA from structural correspondence. GENERAL SIGNIFICANCE Motional dynamics can be a powerful tool to efficiently study the mode of DNA binding to proteins that interact differentially with a plethora of DNA sequences, even in the absence of structural breakthrough.
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Affiliation(s)
- Anwesha Biswas
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, Maharashtra 400076, India
| | - Satya Narayan
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, Maharashtra 400005, India
| | - Mamata V Kallianpur
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, Maharashtra 400005, India
| | - G Krishnamoorthy
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, Maharashtra 400005, India.
| | - Ruchi Anand
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, Maharashtra 400076, India.
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Biarnes-Carrera M, Breitling R, Takano E. Butyrolactone signalling circuits for synthetic biology. Curr Opin Chem Biol 2015; 28:91-8. [PMID: 26164547 DOI: 10.1016/j.cbpa.2015.06.024] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 06/16/2015] [Accepted: 06/20/2015] [Indexed: 01/14/2023]
Abstract
Signalling circuits based on quorum sensing mechanisms have been popular tools for synthetic biology. Recent advances in our understanding of the analogous systems regulating antibiotics production in soil bacteria suggest that these might provide useful complementary tools to increase the complexity of possible circuit designs. Here we discuss the diversity of these natural circuits, which use γ-butyrolactones (GBLs) as their main inter-cellular signal, highlighting the range of new building blocks they could provide, as well as a number of exciting recent applications of GBL-based circuits in heterologous systems. We conclude by presenting examples of the novel circuit complexity that could become accessible through the use of GBL-based designs.
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Affiliation(s)
- Marc Biarnes-Carrera
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Rainer Breitling
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Eriko Takano
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom.
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18
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Ghisaidoobe ABT, Chung SJ. Intrinsic tryptophan fluorescence in the detection and analysis of proteins: a focus on Förster resonance energy transfer techniques. Int J Mol Sci 2014; 15:22518-38. [PMID: 25490136 PMCID: PMC4284722 DOI: 10.3390/ijms151222518] [Citation(s) in RCA: 517] [Impact Index Per Article: 51.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 11/08/2014] [Accepted: 11/18/2014] [Indexed: 12/18/2022] Open
Abstract
Förster resonance energy transfer (FRET) occurs when the distance between a donor fluorophore and an acceptor is within 10 nm, and its application often necessitates fluorescent labeling of biological targets. However, covalent modification of biomolecules can inadvertently give rise to conformational and/or functional changes. This review describes the application of intrinsic protein fluorescence, predominantly derived from tryptophan (λ EX ≈ 280 nm, λ EM ≈ 350 nm), in protein-related research and mainly focuses on label-free FRET techniques. In terms of wavelength and intensity, tryptophan fluorescence is strongly influenced by its (or the proteinlocal environment, which, in addition to fluorescence quenching, has been applied to study protein conformational changes. Intrinsic Förster resonance energy transfer (iFRET), a recently developed technique, utilizes the intrinsic fluorescence of tryptophan in conjunction with target-specific fluorescent probes as FRET donors and acceptors, respectively, for real time detection of native proteins.
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Affiliation(s)
| | - Sang J Chung
- Department of Chemistry, Dongguk University, Seoul 100-715, Korea.
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