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Kraševec N, Panevska A, Lemež Š, Razinger J, Sepčić K, Anderluh G, Podobnik M. Lipid-Binding Aegerolysin from Biocontrol Fungus Beauveria bassiana. Toxins (Basel) 2021; 13:820. [PMID: 34822604 PMCID: PMC8624791 DOI: 10.3390/toxins13110820] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/15/2021] [Accepted: 11/17/2021] [Indexed: 11/16/2022] Open
Abstract
Fungi are the most common pathogens of insects and thus important regulators of their populations. Lipid-binding aegerolysin proteins, which are commonly found in the fungal kingdom, may be involved in several biologically relevant processes including attack and defense against other organisms. Aegerolysins act alone or together with membrane-attack-complex/perforin (MACPF)-like proteins to form transmembrane pores that lead to cell lysis. We performed an in-depth bioinformatics analysis of aegerolysins in entomopathogenic fungi and selected a candidate aegerolysin, beauveriolysin A (BlyA) from Beauveria bassiana. BlyA was expressed as a recombinant protein in Escherichia coli, and purified to further determine its functional and structural properties, including lipid-binding ability. Aegerolysins were found to be encoded in genomes of entomopathogenic fungi, such as Beauveria, Cordyceps, Metarhizium and Ophiocordyceps. Detailed bioinformatics analysis revealed that they are linked to MACPF-like genes in most genomes. We also show that BlyA interacts with an insect-specific membrane lipid. These results were placed in the context of other fungal and bacterial aegerolysins and their partner proteins. We believe that aegerolysins play a role in promoting the entomopathogenic and antagonistic activity of B. bassiana, which is an active ingredient of bioinsecticides.
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Affiliation(s)
- Nada Kraševec
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, SI-1000 Ljubljana, Slovenia; (Š.L.); (G.A.); (M.P.)
| | - Anastasija Panevska
- Department of Biology, Biotechnical Faculty, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (A.P.); (K.S.)
| | - Špela Lemež
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, SI-1000 Ljubljana, Slovenia; (Š.L.); (G.A.); (M.P.)
- Biotechnology, Biotechnical Faculty, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Jaka Razinger
- Plant Protection Department, Agricultural Institute of Slovenia, Hacquetova 17, SI-1000 Ljubljana, Slovenia;
| | - Kristina Sepčić
- Department of Biology, Biotechnical Faculty, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (A.P.); (K.S.)
| | - Gregor Anderluh
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, SI-1000 Ljubljana, Slovenia; (Š.L.); (G.A.); (M.P.)
| | - Marjetka Podobnik
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, SI-1000 Ljubljana, Slovenia; (Š.L.); (G.A.); (M.P.)
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Mohanty L, Mishra C, Pradhan SK, Mishra SR, Nayak G. Identification of novel polymorphism and in silico analysis of caprine DNAJB3 gene. Small Rumin Res 2021. [DOI: 10.1016/j.smallrumres.2021.106492] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Kumashiro M, Izumi Y, Matsuo K. Conformation of myelin basic protein bound to phosphatidylinositol membrane characterized by vacuum-ultraviolet circular-dichroism spectroscopy and molecular-dynamics simulations. Proteins 2021; 89:1251-1261. [PMID: 33998060 DOI: 10.1002/prot.26146] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 05/07/2021] [Indexed: 12/18/2022]
Abstract
The 18.5-kDa isoform of myelin basic protein (MBP) interacts with the membrane surface of the myelin sheath to construct its compact multilamellar structure. This study characterized the conformation of MBP in the membrane by measuring the vacuum-ultraviolet circular-dichroism (VUVCD) spectra of MBP in the bilayer liposome comprising the following essential lipid constituents of the myelin sheath: phosphatidylinositol (PI), phosphatidylinositol-4-phosphate (PIP), and phosphatidylinositol-4,5-bisphosphate (PIP2). The spectra of MBP exhibited the characteristic peaks of the helix structure in the presence of PI liposome, and the intensity increased markedly in the presence of PIP and PIP2 liposomes to show an isodichroic point. This suggests that the amount of the membrane-bound conformation of MBP enhanced due to the increased number of negative net charges on the liposome surfaces. Secondary-structure analysis revealed that MBP in the membrane comprised approximately 40% helix contents and eight helix segments. Molecular-dynamics (MD) simulations of the eight segments were conducted for 250 ns in the presence of PI membrane, which predicted two amphiphilic and three nonamphiphilic helices as the membrane-interaction sites. Further analysis of the distances of the amino-acid residues in each segment from the phosphate group suggested that the nonamphiphilic helices interact with the membrane surface electrostatically, while the amphiphilic ones invade the inside of the membrane to produce electrostatic and hydrophobic interactions. These results show that MBP can interact with the PI membrane via amphiphilic and nonamphiphilic helices under the control of a delicate balance between electrostatic and hydrophobic interactions.
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Affiliation(s)
- Munehiro Kumashiro
- Department of Physical Science, Graduate School of Science, Hiroshima University, Hiroshima, Japan
| | - Yudai Izumi
- Hiroshima Synchrotron Radiation Center, Hiroshima University, Hiroshima, Japan
| | - Koichi Matsuo
- Hiroshima Synchrotron Radiation Center, Hiroshima University, Hiroshima, Japan
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Kraševec N, Novak M, Barat S, Skočaj M, Sepčić K, Anderluh G. Unconventional Secretion of Nigerolysins A from Aspergillus Species. Microorganisms 2020; 8:E1973. [PMID: 33322461 PMCID: PMC7763983 DOI: 10.3390/microorganisms8121973] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/04/2020] [Accepted: 12/09/2020] [Indexed: 01/05/2023] Open
Abstract
Aegerolysins are small lipid-binding proteins particularly abundant in fungi. Aegerolysins from oyster mushrooms interact with an insect-specific membrane lipid and, together with MACPF proteins produced by the same organism, form pesticidal pore-forming complexes. The specific interaction with the same membrane lipid was recently demonstrated for nigerolysin A2 (NigA2), an aegerolysin from Aspergillus niger. In Aspergillus species, the aegerolysins were frequently found as secreted proteins, indicating their function in fungal defense. Using immunocytochemistry and live-cell imaging we investigated the subcellular localization of the nigerolysins A in A. niger, while their secretion was addressed by secretion prediction and Western blotting. We show that both nigerolysins A are leaderless proteins that reach the cell exterior by an unconventional protein secretion. NigA proteins are evenly distributed in the cytoplasm of fungal hyphae. A detailed bioinformatics analysis of Aspergillus aegerolysins suggests that the same function occurs only in a limited number of aegerolysins. From alignment, analysis of chromosomal loci, orthology, synteny, and phylogeny it follows that the same or a similar function described for pairs of pesticidal proteins of Pleurotus sp. can be expected in species of the subgenus Circumdati, section Nigri, series Nigri, and some other species with adjacent pairs of putative pesticidal proteins.
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Affiliation(s)
- Nada Kraševec
- National Institute of Chemistry, SI-1000 Ljubljana, Slovenia; (S.B.); (G.A.)
| | - Maruša Novak
- Department of Biology, Biotechnical Faculty, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (M.N.); (M.S.); (K.S.)
| | - Simona Barat
- National Institute of Chemistry, SI-1000 Ljubljana, Slovenia; (S.B.); (G.A.)
- Department of Biology, Biotechnical Faculty, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (M.N.); (M.S.); (K.S.)
| | - Matej Skočaj
- Department of Biology, Biotechnical Faculty, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (M.N.); (M.S.); (K.S.)
| | - Kristina Sepčić
- Department of Biology, Biotechnical Faculty, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (M.N.); (M.S.); (K.S.)
| | - Gregor Anderluh
- National Institute of Chemistry, SI-1000 Ljubljana, Slovenia; (S.B.); (G.A.)
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Mandal M, Mishra C, Dash SK, Swain LL, Pradhan SK, Nayak G. Identification and futuristic role of novel polymorphism of caprine PrP gene. Anim Biotechnol 2020; 33:53-62. [PMID: 32427042 DOI: 10.1080/10495398.2020.1765789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The Caprine Prion Protein (PrP) gene polymorphism in three different native Indian goat populations of Southern Odisha, namely Ganjam (a registered breed of India), Ghumusari and Raighar was studied. The 876 bp amplified segment of PrP gene contains full length coding sequence of 771 bp. In Ganjam and Ghumusari goats, any difference of nucleotide sequence was not identified. However, the comparison of nucleotide sequences of Raighar goats and goats of other locality revealed a change in nucleotide at five different positions (G190A, G724A, A727T, C775G and C800T) which includes two non-synonymous nucleotide changes. The non-synonymous nucleotide change resulted a change in amino acid at two different positions (Ser234Cys and Lys246Phe) in mature polypeptide which were not reported earlier and therefore, considered as novel. On the basis of these variants of PrP gene phylogenetic tree was constructed which showed that Ganjam and Raighar goats appeared in different clade. Since any occurrence of Scrapie infection in goats of Odisha was not reported, it can be proposed that these changes in amino acid may be responsible as resistance allele.
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Affiliation(s)
- Manaswini Mandal
- Department of Animal Breeding and Genetics, Orissa University of Agriculture and Technology, Bhubaneswar, India
| | - Chinmoy Mishra
- Department of Animal Breeding and Genetics, Orissa University of Agriculture and Technology, Bhubaneswar, India
| | - Susant Kumar Dash
- Department of Animal Breeding and Genetics, Orissa University of Agriculture and Technology, Bhubaneswar, India
| | - Lipi Lekha Swain
- Department of Animal Breeding and Genetics, Orissa University of Agriculture and Technology, Bhubaneswar, India
| | - Sukanta Kumar Pradhan
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar, India
| | - Gangadhar Nayak
- Department of Animal Breeding and Genetics, Orissa University of Agriculture and Technology, Bhubaneswar, India
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In silico analysis of caprine superoxide dismutase 1 (SOD1) gene. Genomics 2020; 112:212-217. [DOI: 10.1016/j.ygeno.2019.01.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Accepted: 01/22/2019] [Indexed: 01/18/2023]
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Swain LL, Mishra C, Sahoo SS, Nayak G, Pradhan SK, Mishra SR, Dige M. An in vivo and in silico analysis of novel variation in TMBIM6 gene affecting cardiopulmonary traits of Indian goats. J Therm Biol 2019; 88:102491. [PMID: 32125979 DOI: 10.1016/j.jtherbio.2019.102491] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 11/30/2019] [Accepted: 12/23/2019] [Indexed: 01/17/2023]
Abstract
Transmembrane Bax Inhibitor Motif-containing 6 (TMBIM6) gene acts as calcium leak channel and negatively regulates autophagy and autophagosome formation. The TMBIM6 gene was amplified and searched for variation in three different goat populations (i.e. Black Bengal, Ganjam and Raighar) of Odisha state of the India. The result indicated two substitutions i.e. 55th position (C55T) and 95th position (C95A) in the amplified region of the gene resulting in change of amino acids (Leu > Phe and Thr > Asn). The identified SNPs were combined to form haplotypes and animals were grouped accordingly. Structural analysis showed minor changes (5%) in between mutant and wild TMBIM6 protein structures. However, any functional variation could not be identified with respect to the calcium ligand and open pore state. But an alteration of calcium binding site was found. The binding interaction of calcium with the TMBIM6 protein was hydrophobic in nature in closed state whereas hydrophilic in open pore stage. The stress releasing function was the result of calcium leakage controlled by amino acids coded by exon 4 and exon 5 regions of TMBIM6 gene. The effect of breed and haplotype on cardiopulmonary traits was studied. The data on cardiopulmonary traits of body i.e. rectal temperature, skin temperature, heart rate and respiration rate were recorded when ambient temperature usually remained the highest. The statistical analysis showed, significant difference in rectal temperature, skin temperature and respiration rate among these goat populations. The haplotypes (CC and TA) were found to have a significant (P < 0.05) effect on rectal temperature, skin temperature and respiration rate. However, any such significant effect could not be identified in recorded heart rate. The objective of the present study to identify the genetic variations in TMBIM6 gene having significant effect on cardiopulmonary traits which can be further uses as the molecular markers to improve heat tolerance mechanism in goats.
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Affiliation(s)
- Lipi Lekha Swain
- Department of Animal Breeding and Genetics, Orissa University of Agriculture and Technology, Bhubaneswar, India.
| | - Chinmoy Mishra
- Department of Animal Breeding and Genetics, Orissa University of Agriculture and Technology, Bhubaneswar, India.
| | - Siddhant Sekhar Sahoo
- Department of Animal Breeding and Genetics, National Dairy Research Institute, Karnal, India.
| | - Gangadhar Nayak
- Department of Animal Breeding and Genetics, Orissa University of Agriculture and Technology, Bhubaneswar, India.
| | - Sukanta Kumar Pradhan
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar, India.
| | - Smruti Ranjan Mishra
- Department of Veterinary Physiology, Orissa University of Agriculture and Technology, Bhubaneswar, India.
| | - Mahesh Dige
- Department of Animal Genetics, Central Institute for Research on Goats, Makhdoom, Mathura, India.
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Structural Analysis and Dynamic Processes of the Transmembrane Segment Inside Different Micellar Environments-Implications for the TM4 Fragment of the Bilitranslocase Protein. Int J Mol Sci 2019; 20:ijms20174172. [PMID: 31454948 PMCID: PMC6747479 DOI: 10.3390/ijms20174172] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 08/18/2019] [Accepted: 08/20/2019] [Indexed: 12/22/2022] Open
Abstract
The transmembrane (TM) proteins are gateways for molecular transport across the cell membrane that are often selected as potential targets for drug design. The bilitranslocase (BTL) protein facilitates the uptake of various anions, such as bilirubin, from the blood into the liver cells. As previously established, there are four hydrophobic transmembrane segments (TM1-TM4), which constitute the structure of the transmembrane channel of the BTL protein. In our previous studies, the 3D high-resolution structure of the TM2 and TM3 transmembrane fragments of the BTL in sodium dodecyl sulfate (SDS) micellar media were solved using Nuclear Magnetic Resonance (NMR) spectroscopy and molecular dynamics simulations (MD). The high-resolution 3D structure of the fourth transmembrane region (TM4) of the BTL was evaluated using NMR spectroscopy in two different micellar media, anionic SDS and zwitterionic DPC (dodecylphosphocholine). The presented experimental data revealed the existence of an α -helical conformation in the central part of the TM4 in both micellar media. In the case of SDS surfactant, the α -helical conformation is observed for the Pro258-Asn269 region. The use of the zwitterionic DPC micelle leads to the formation of an amphipathic α -helix, which is characterized by the extension of the central α -helix in the TM4 fragment to Phe257-Thr271. The complex character of the dynamic processes in the TM4 peptide within both surfactants was analyzed based on the relaxation data acquired on 15 N and 31 P isotopes. Contrary to previously published and present observations in the SDS micelle, the zwitterionic DPC environment leads to intensive low-frequency molecular dynamic processes in the TM4 fragment.
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Venko K, Roy Choudhury A, Novič M. Computational Approaches for Revealing the Structure of Membrane Transporters: Case Study on Bilitranslocase. Comput Struct Biotechnol J 2017; 15:232-242. [PMID: 28228927 PMCID: PMC5312651 DOI: 10.1016/j.csbj.2017.01.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 01/19/2017] [Accepted: 01/20/2017] [Indexed: 11/23/2022] Open
Abstract
The structural and functional details of transmembrane proteins are vastly underexplored, mostly due to experimental difficulties regarding their solubility and stability. Currently, the majority of transmembrane protein structures are still unknown and this present a huge experimental and computational challenge. Nowadays, thanks to X-ray crystallography or NMR spectroscopy over 3000 structures of membrane proteins have been solved, among them only a few hundred unique ones. Due to the vast biological and pharmaceutical interest in the elucidation of the structure and the functional mechanisms of transmembrane proteins, several computational methods have been developed to overcome the experimental gap. If combined with experimental data the computational information enables rapid, low cost and successful predictions of the molecular structure of unsolved proteins. The reliability of the predictions depends on the availability and accuracy of experimental data associated with structural information. In this review, the following methods are proposed for in silico structure elucidation: sequence-dependent predictions of transmembrane regions, predictions of transmembrane helix–helix interactions, helix arrangements in membrane models, and testing their stability with molecular dynamics simulations. We also demonstrate the usage of the computational methods listed above by proposing a model for the molecular structure of the transmembrane protein bilitranslocase. Bilitranslocase is bilirubin membrane transporter, which shares similar tissue distribution and functional properties with some of the members of the Organic Anion Transporter family and is the only member classified in the Bilirubin Transporter Family. Regarding its unique properties, bilitranslocase is a potentially interesting drug target.
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Affiliation(s)
- Katja Venko
- Department of Cheminformatics, National Institute of Chemistry, Ljubljana, Slovenia
| | - A Roy Choudhury
- Department of Cheminformatics, National Institute of Chemistry, Ljubljana, Slovenia
| | - Marjana Novič
- Department of Cheminformatics, National Institute of Chemistry, Ljubljana, Slovenia
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Choudhury AR, Sikorska E, van den Boom J, Bayer P, Popenda Ł, Szutkowski K, Jurga S, Bonomi M, Sali A, Zhukov I, Passamonti S, Novič M. Structural Model of the Bilitranslocase Transmembrane Domain Supported by NMR and FRET Data. PLoS One 2015; 10:e0135455. [PMID: 26291722 PMCID: PMC4546402 DOI: 10.1371/journal.pone.0135455] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 07/22/2015] [Indexed: 11/19/2022] Open
Abstract
We present a 3D model of the four transmembrane (TM) helical regions of bilitranslocase (BTL), a structurally uncharacterized protein that transports organic anions across the cell membrane. The model was computed by considering helix-helix interactions as primary constraints, using Monte Carlo simulations. The interactions between the TM2 and TM3 segments have been confirmed by Förster resonance energy transfer (FRET) spectroscopy and nuclear magnetic resonance (NMR) spectroscopy, increasing our confidence in the model. Several insights into the BTL transport mechanism were obtained by analyzing the model. For example, the observed cis-trans Leu-Pro peptide bond isomerization in the TM3 fragment may indicate a key conformational change during anion transport by BTL. Our structural model of BTL may facilitate further studies, including drug discovery.
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Affiliation(s)
| | | | - Johannes van den Boom
- Institute for Structural and Medicinal Biochemistry, Center for Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Peter Bayer
- Institute for Structural and Medicinal Biochemistry, Center for Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Łukasz Popenda
- NanoBioMedical Center, Adam Mickiewicz University, Poznań, Poland
| | - Kosma Szutkowski
- NanoBioMedical Center, Adam Mickiewicz University, Poznań, Poland
- Faculty of Physics, Adam Mickiewicz University, Poznań, Poland
| | - Stefan Jurga
- NanoBioMedical Center, Adam Mickiewicz University, Poznań, Poland
- Faculty of Physics, Adam Mickiewicz University, Poznań, Poland
| | - Massimiliano Bonomi
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, University of California, San Francisco, California, United States of America
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, University of California, San Francisco, California, United States of America
| | - Igor Zhukov
- NanoBioMedical Center, Adam Mickiewicz University, Poznań, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
- * E-mail: (MN); (SP); (IZ)
| | - Sabina Passamonti
- Department of Life Sciences, University of Trieste, Trieste, Italy
- * E-mail: (MN); (SP); (IZ)
| | - Marjana Novič
- National Institute of Chemistry, Hajdrihova 19, Ljubljana, Slovenia
- * E-mail: (MN); (SP); (IZ)
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Adrover M, Sanchis P, Vilanova B, Pauwels K, Martorell G, Pérez JJ. Conformational ensembles of neuromedin C reveal a progressive coil-helix transition within a binding-induced folding mechanism. RSC Adv 2015. [DOI: 10.1039/c5ra12753j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
NMR has been used to elucidate the folding pathway of neuromedin C and to characterize the architecture of the NMC–SDS micelle complex. Its C-terminal region is more prone to acquire an α-helical fold than the N-terminus, and it also binds to micelles.
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Affiliation(s)
- Miquel Adrover
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS)
- Departament de Química
- Universitat de les Illes Balears (UIB)
- Palma de Mallorca
- Spain
| | - Pilar Sanchis
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS)
- Departament de Química
- Universitat de les Illes Balears (UIB)
- Palma de Mallorca
- Spain
| | - Bartolomé Vilanova
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS)
- Departament de Química
- Universitat de les Illes Balears (UIB)
- Palma de Mallorca
- Spain
| | - Kris Pauwels
- Structural Biology Brussels
- Vrije Universiteit Brussels (VUB)
- 1050 Brussels
- Belgium
- Structural Biology Research Centre
| | - Gabriel Martorell
- Serveis Científico-Tècnics
- Universitat de les Illes Balears (UIB)
- Palma de Mallorca
- Spain
| | - Juan Jesús Pérez
- Departament d'Enginyeria Química
- Universitat Politecnica de Catalunya (UPC)
- ETSEIB
- Barcelona
- Spain
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Martinčič R, Venko K, Župerl Š, Novič M. Chemometrics approach for the prediction of structure-activity relationship for membrane transporter bilitranslocase. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2014; 25:853-872. [PMID: 25337672 DOI: 10.1080/1062936x.2014.962082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Membrane transport proteins are essential for cellular uptake of numerous salts, nutrients and drugs. Bilitranslocase is a transporter, specific for water-soluble organic anions, and is the only known carrier of nucleotides and nucleotide-like compounds. Experimental data of bilitranslocase ligand specificity for 120 compounds were used to construct classification models using counter-propagation artificial neural networks (CP-ANNs) and support vector machines (SVMs). A subset of active compounds with experimentally determined transport rates was used to build predictive QSAR models for estimation of transport rates of unknown compounds. Several modelling methods and techniques were applied, i.e. CP-ANN, genetic algorithm, self-organizing mapping and multiple linear regression method. The best predictions were achieved using CP-ANN coupled with a genetic algorithm, with the external validation parameter QV(2) of 0.96. The applicability domains of the models were defined to determine the chemical space in which reliable predictions can be obtained. The models were applied for the estimation of bilitranslocase transport activity for two sets of pharmaceutically interesting compounds, antioxidants and antiprions. We found that the relative planarity and a high potential for hydrogen bond formation are the common structural features of anticipated substrates of bilitranslocase. These features may serve as guidelines in the design of new pharmaceuticals transported by bilitranslocase.
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Affiliation(s)
- R Martinčič
- a Laboratory of Chemometrics , National Institute of Chemistry , Ljubljana , Slovenia
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Peresson C, Petrussa E, Filippi A, Tramer F, Passamonti S, Rajcevic U, Montanič S, Terdoslavich M, Čurin Šerbec V, Vianello A, Braidot E. Involvement of mammalian bilitranslocase-like protein(s) in chlorophyll catabolism of Pisum sativum L. tissues. J Bioenerg Biomembr 2014; 46:109-17. [PMID: 24510308 DOI: 10.1007/s10863-014-9539-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 01/16/2014] [Indexed: 10/25/2022]
Abstract
Putative pea bilin and cyclic tetrapyrrole transporter proteins were identified by means of an antibody raised against a bilirubin-interacting aminoacidic sequence of mammalian bilitranslocase (TC No. 2.A.65.1.1). The immunochemical approach showed the presence of several proteins mostly in leaf microsomal, chloroplast and tonoplast vesicles. In these membrane fractions, electrogenic bromosulfalein transport activity was also monitored, being specifically inhibited by anti-bilitranslocase sequence antibody. Moreover, the inhibition of transport activity in pea leaf chloroplast vesicles, by both the synthetic cyclic tetrapyrrole chlorophyllin and the heme catabolite biliverdin, supports the involvement of some of these proteins in the transport of linear/cyclic tetrapyrroles during chlorophyll metabolism. Immunochemical localization in chloroplast sub-compartments revealed that these putative bilitranslocase-like transporters are restricted to the thylakoids only, suggesting their preferential implication in the uptake of cyclic tetrapyrrolic intermediates from the stroma during chlorophyll biosynthesis. Finally, the presence of a conserved bilin-binding sequence in different proteins (enzymes and transporters) from divergent species is discussed in an evolutionary context.
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Affiliation(s)
- Carlo Peresson
- Department of Agricultural and Environmental Sciences, Section of Plant Biology, University of Udine, Via delle Scienze 91, 33100, Udine, Italy
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Structural elucidation of transmembrane transporter protein bilitranslocase: Conformational analysis of the second transmembrane region TM2 by molecular dynamics and NMR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2609-19. [DOI: 10.1016/j.bbamem.2013.06.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 05/31/2013] [Accepted: 06/06/2013] [Indexed: 11/22/2022]
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