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The Pentose Phosphate Pathway in Yeasts-More Than a Poor Cousin of Glycolysis. Biomolecules 2021; 11:biom11050725. [PMID: 34065948 PMCID: PMC8151747 DOI: 10.3390/biom11050725] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/04/2021] [Accepted: 05/10/2021] [Indexed: 01/14/2023] Open
Abstract
The pentose phosphate pathway (PPP) is a route that can work in parallel to glycolysis in glucose degradation in most living cells. It has a unidirectional oxidative part with glucose-6-phosphate dehydrogenase as a key enzyme generating NADPH, and a non-oxidative part involving the reversible transketolase and transaldolase reactions, which interchange PPP metabolites with glycolysis. While the oxidative branch is vital to cope with oxidative stress, the non-oxidative branch provides precursors for the synthesis of nucleic, fatty and aromatic amino acids. For glucose catabolism in the baker’s yeast Saccharomyces cerevisiae, where its components were first discovered and extensively studied, the PPP plays only a minor role. In contrast, PPP and glycolysis contribute almost equally to glucose degradation in other yeasts. We here summarize the data available for the PPP enzymes focusing on S. cerevisiae and Kluyveromyces lactis, and describe the phenotypes of gene deletions and the benefits of their overproduction and modification. Reference to other yeasts and to the importance of the PPP in their biotechnological and medical applications is briefly being included. We propose future studies on the PPP in K. lactis to be of special interest for basic science and as a host for the expression of human disease genes.
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Kumar Nagarajan S, Babu S, Sohn H, Devaraju P, Madhavan T. Toward a better understanding of the interaction between somatostatin receptor 2 and its ligands: a structural characterization study using molecular dynamics and conceptual density functional theory. J Biomol Struct Dyn 2018; 37:3081-3102. [PMID: 30079808 DOI: 10.1080/07391102.2018.1508368] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
This study is a part of the extensive research intending to provide the structural insights on somatostatin and its receptor. Herein, we have studied the structural complexity involved in the binding of somatostatin receptor 2 (SSTR2) with its agonists and antagonist. A 3D QSAR study based on comparative molecular field analysis and comparative molecular similarity analysis (CoMSIA) discerned that a SSTR2 ligand with electronegative, less-bulkier, and hydrogen atom donating/accepting substitutions is important for their biological activity. A conceptual density functional theory (DFT) study was followed to study the chemical behavior of the ligands based on the molecular descriptors derived using the Fukui's molecular orbital theory. We have performed molecular dynamics simulations of receptor-ligand complexes for 100 ns to analyze the dynamic stability of the backbone Cα atoms of the receptor and strength and approachability of the receptor-ligand complex. The findings of this study could be efficacious in the further studies understanding intricate structural features of the somatostatin receptors and in discovering novel subtype-specific ligands with higher affinity. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Santhosh Kumar Nagarajan
- a Department of Genetic Engineering School of Bioengineering , SRM Institute of Science and Technology , Kattankulathur, Chennai , India
| | - Sathya Babu
- a Department of Genetic Engineering School of Bioengineering , SRM Institute of Science and Technology , Kattankulathur, Chennai , India
| | - Honglae Sohn
- b Department of Chemistry and Department of Carbon Materials , Chosun University , Gwangju , South Korea
| | - Panneer Devaraju
- c Division of Microbiology and Molecular Biology , Vector Control Research Centre, Indian Council of Medical Research , Pondicherry , India
| | - Thirumurthy Madhavan
- a Department of Genetic Engineering School of Bioengineering , SRM Institute of Science and Technology , Kattankulathur, Chennai , India
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Balasubramanian A, Bhattacharjee M, Sakthivel M, Thirumavalavan M, Madhavan T, Nagarajan SK, Palaniyandi V, Raman P. Isolation, purification and characterization of proteinaceous fungal α-amylase inhibitor from rhizome of Cheilocostus speciosus (J.Koenig) C.D.Specht. Int J Biol Macromol 2018; 111:39-51. [PMID: 29305211 DOI: 10.1016/j.ijbiomac.2017.12.158] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 12/27/2017] [Accepted: 12/29/2017] [Indexed: 11/18/2022]
Abstract
As the aim of this present study, a proteinaceous α-amylase inhibitor has been isolated from the rhizome of Cheilocostus specious (C. speciosus) and was purified using DEAE cellulose anion exchange chromatography followed by gel filtration using Sephacryl-S-200 column. The purity and molecular mass of the purified inhibitor was determined by SDS-PAGE and LC-MS respectively. The molecular mass of the purified inhibitor was determined to be 31.18kDa. Protein-protein docking was also carried out as molecular model. Model validation methods such as Ramachandran plot and Z-score plot were adopted to validate the structural description (sequence analysis) of proteins. The inhibitory activity was confirmed using spectrophotometric and reverse zymogram analyses. This 31.18kDa protein from C. speciosus inhibited the activity of fungal α-amylase by 71% at the level of ion exchange chromatography and 96% after gel filtration. The inhibition activity of the α-amylase inhibitor was stable and high at optimum pH6 (52.2%) and temperatures of 30-40°C (72.2%). Thus it was suggested that the main responsible for the versatile biological and pharmacological activities of C. speciosus is due to its primary metabolites (proteins) only.
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Affiliation(s)
- Abinaya Balasubramanian
- Department of Biotechnology, School of Bioengineering, SRM University, Kattankulathur 603203, Tamilnadu, India
| | - Manish Bhattacharjee
- Department of Biotechnology, School of Bioengineering, SRM University, Kattankulathur 603203, Tamilnadu, India
| | - Meenakumari Sakthivel
- Department of Biotechnology, School of Bioengineering, SRM University, Kattankulathur 603203, Tamilnadu, India
| | - Munusamy Thirumavalavan
- Graduate Institute of Environmental Engineering, National Central University, Chungli, Taoyuan County 320, Taiwan.
| | - Thirumurthy Madhavan
- Department of Genetic Engineering, School of Bioengineering, SRM University, Kattankulathur 603203, Tamilnadu, India
| | - Santhosh Kumar Nagarajan
- Department of Genetic Engineering, School of Bioengineering, SRM University, Kattankulathur 603203, Tamilnadu, India
| | - Velusamy Palaniyandi
- Department of Biotechnology, School of Bioengineering, SRM University, Kattankulathur 603203, Tamilnadu, India
| | - Pachaiappan Raman
- Department of Biotechnology, School of Bioengineering, SRM University, Kattankulathur 603203, Tamilnadu, India; Metabolomics, Proteomics and Mass Spectrometry Core Facilities, EEJMRB, 15 N Medical Drive East RM A306 (Basement), University of Utah, Salt Lake City, UT 84112-5650, USA.
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Theoretical analysis of somatostatin receptor 5 with antagonists and agonists for the treatment of neuroendocrine tumors. Mol Divers 2017. [PMID: 28155055 DOI: 10.1007/s11030‐016‐9722‐7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
We report on SSTR5 receptor modeling and its interaction with reported antagonist and agonist molecules. Modeling of the SSTR5 receptor was carried out using multiple templates with the aim of improving the precision of the generated models. The selective SSTR5 antagonists, agonists and native somatostatin SRIF-14 were employed to propose the binding site of SSTR5 and to identify the critical residues involved in the interaction of the receptor with other molecules. Residues Q2.63, D3.32, Q3.36, C186, Y7.34 and Y7.42 were found to be highly significant for their strong interaction with the receptor. SSTR5 antagonists were utilized to perform a 3D quantitative structure-activity relationship study. A comparative molecular field analysis (CoMFA) was conducted using two different alignment schemes, namely the ligand-based and receptor-based alignment methods. The best statistical results were obtained for ligand-based ([Formula: see text], [Formula: see text] = 0.988, noc = 4) and receptor-guided methods (docked mode 1:[Formula: see text], [Formula: see text], noc = 5), (docked mode 2:[Formula: see text] = 0.555, [Formula: see text], noc = 5). Based on CoMFA contour maps, an electropositive substitution at [Formula: see text], [Formula: see text] and [Formula: see text] position and bulky group at [Formula: see text] position are important in enhancing molecular activity.
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Theoretical analysis of somatostatin receptor 5 with antagonists and agonists for the treatment of neuroendocrine tumors. Mol Divers 2017; 21:367-384. [PMID: 28155055 DOI: 10.1007/s11030-016-9722-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 12/30/2016] [Indexed: 10/20/2022]
Abstract
We report on SSTR5 receptor modeling and its interaction with reported antagonist and agonist molecules. Modeling of the SSTR5 receptor was carried out using multiple templates with the aim of improving the precision of the generated models. The selective SSTR5 antagonists, agonists and native somatostatin SRIF-14 were employed to propose the binding site of SSTR5 and to identify the critical residues involved in the interaction of the receptor with other molecules. Residues Q2.63, D3.32, Q3.36, C186, Y7.34 and Y7.42 were found to be highly significant for their strong interaction with the receptor. SSTR5 antagonists were utilized to perform a 3D quantitative structure-activity relationship study. A comparative molecular field analysis (CoMFA) was conducted using two different alignment schemes, namely the ligand-based and receptor-based alignment methods. The best statistical results were obtained for ligand-based ([Formula: see text], [Formula: see text] = 0.988, noc = 4) and receptor-guided methods (docked mode 1:[Formula: see text], [Formula: see text], noc = 5), (docked mode 2:[Formula: see text] = 0.555, [Formula: see text], noc = 5). Based on CoMFA contour maps, an electropositive substitution at [Formula: see text], [Formula: see text] and [Formula: see text] position and bulky group at [Formula: see text] position are important in enhancing molecular activity.
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Nauton L, Hélaine V, Théry V, Hecquet L. Insights into the Thiamine Diphosphate Enzyme Activation Mechanism: Computational Model for Transketolase Using a Quantum Mechanical/Molecular Mechanical Method. Biochemistry 2016; 55:2144-52. [PMID: 26998737 DOI: 10.1021/acs.biochem.5b00787] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We propose the first computational model for transketolase (TK), a thiamine diphosphate (ThDP)-dependent enzyme, using a quantum mechanical/molecular mechanical method on the basis of crystallographic TK structures from yeast and Escherichia coli, together with experimental kinetic data reported in the literature with wild-type and mutant TK. This model allowed us to define a new route for ThDP activation in the enzyme environment. We evidenced a strong interaction between ThDP and Glu418B of the TK active site, itself stabilized by Glu162A. The crucial point highlighted here is that deprotonation of ThDP C2 is not performed by ThDP N4' as reported in the literature, but by His481B, involving a HOH688A molecule bridge. Thus, ThDP N4' is converted from an amino form to an iminium form, ensuring the stabilization of the C2 carbanion or carbene. Finally, ThDP activation proceeds via an intermolecular process and not by an intramolecular one as reported in the literature. More generally, this proposed ThDP activation mechanism can be applied to some other ThDP-dependent enzymes and used to define the entire TK mechanism with donor and acceptor substrates more accurately.
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Affiliation(s)
- Lionel Nauton
- Université Clermont Auvergne, Université Blaise-Pascal , Institut de Chimie de Clermont-Ferrand, BP 10448, F-63000 Clermont-Ferrand, France.,CNRS , UMR 6296, ICCF, F-63178 Aubiere, France
| | - Virgil Hélaine
- Université Clermont Auvergne, Université Blaise-Pascal , Institut de Chimie de Clermont-Ferrand, BP 10448, F-63000 Clermont-Ferrand, France.,CNRS , UMR 6296, ICCF, F-63178 Aubiere, France
| | - Vincent Théry
- Université Clermont Auvergne, Université Blaise-Pascal , Institut de Chimie de Clermont-Ferrand, BP 10448, F-63000 Clermont-Ferrand, France.,CNRS , UMR 6296, ICCF, F-63178 Aubiere, France
| | - Laurence Hecquet
- Université Clermont Auvergne, Université Blaise-Pascal , Institut de Chimie de Clermont-Ferrand, BP 10448, F-63000 Clermont-Ferrand, France.,CNRS , UMR 6296, ICCF, F-63178 Aubiere, France
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Babu S, Nagarajan SK, Lee SH, Madhavan T. Structural characterization of human CRTh2: a combined homology modeling, molecular docking and 3D-QSAR-based in silico approach. Med Chem Res 2016. [DOI: 10.1007/s00044-016-1516-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Purkayastha P, Alokam R, Malapati A, Sriram D, Yogeeswari P. Structural Models for the Design of PKMzeta Inhibitors with Neurobiological Indications. Mol Inform 2015; 34:665-78. [PMID: 27490967 DOI: 10.1002/minf.201500003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 04/01/2015] [Indexed: 11/10/2022]
Abstract
An atypical protein kinase C, PKMzeta has become an attractive target for various neurological disorders including long term potentiation, cognition, neuropathic pain and cancer. Drug discovery efforts have been hindered due to the non-availability of the protein structure and hence in the present study we attempted to build the open and closed models of the protein PKMzeta using homology modeling. The models were then used to identify PKMzeta inhibitors utilizing a high-throughput virtual screening protocol from a large commercial chemical database. Compounds were selected based on the binding interactions and Glide score. Compounds were then subjected to in vitro luminescent based kinase assay for their inhibitory activity on targeted protein. Seven compounds exhibited IC50 s less than or equal to 10 µM. Cell based assays revealed that Lead C3 and Lead C6 exhibited selectivity towards methylmercury treated neuroblastoma growth inhibition and suppressed reactive oxygen species with IC50 s of 0.89 and 0.17 µM, respectively. Furthermore, Lead C3 exhibited attenuation of proinflammatory response with least energy in dynamic simulation studies and thus emerged as a prototypical lead for further development as novel inhibitor of PKMzeta for neurological implications.
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Affiliation(s)
- Priyanka Purkayastha
- Computer-Aided Drug Design Lab, Department of Pharmacy, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Hyderabad-500078, A.P., India phone: +91-40-66303515, +91-40-66303506; fax: +91-40-66303998
| | - Reshma Alokam
- Computer-Aided Drug Design Lab, Department of Pharmacy, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Hyderabad-500078, A.P., India phone: +91-40-66303515, +91-40-66303506; fax: +91-40-66303998
| | - Aruna Malapati
- Department of Computer Science and Information Systems, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Hyderabad-500078, A.P., India
| | - Dharmarajan Sriram
- Computer-Aided Drug Design Lab, Department of Pharmacy, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Hyderabad-500078, A.P., India phone: +91-40-66303515, +91-40-66303506; fax: +91-40-66303998.
| | - Perumal Yogeeswari
- Computer-Aided Drug Design Lab, Department of Pharmacy, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Hyderabad-500078, A.P., India phone: +91-40-66303515, +91-40-66303506; fax: +91-40-66303998.
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Obiol-Pardo C, Alcarraz-Vizán G, Díaz-Moralli S, Cascante M, Rubio-Martinez J. Design of an interface peptide as new inhibitor of human glucose-6-phosphate dehydrogenase. J Mol Graph Model 2014; 49:110-7. [DOI: 10.1016/j.jmgm.2014.02.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 02/18/2014] [Accepted: 02/19/2014] [Indexed: 10/25/2022]
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Maslova AO, Meshalkina LE, Kochetov GA. Computer modeling of transketolase-like protein, TKTL1, a marker of certain tumor tissues. BIOCHEMISTRY (MOSCOW) 2012; 77:296-9. [DOI: 10.1134/s000629791203008x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Obiol-Pardo C, Alcarraz-Vizán G, Cascante M, Rubio-Martinez J. Diphenyl urea derivatives as inhibitors of transketolase: a structure-based virtual screening. PLoS One 2012; 7:e32276. [PMID: 22403640 PMCID: PMC3293897 DOI: 10.1371/journal.pone.0032276] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Accepted: 01/24/2012] [Indexed: 11/28/2022] Open
Abstract
Transketolase is an enzyme involved in a critical step of the non-oxidative branch of the pentose phosphate pathway whose inhibition could lead to new anticancer drugs. Here, we report new human transketolase inhibitors, based on the phenyl urea scaffold, found by applying structure-based virtual screening. These inhibitors are designed to cover a hot spot in the dimerization interface of the homodimer of the enzyme, providing for the first time compounds with a suggested novel binding mode not based on mimicking the thiamine pyrophosphate cofactor.
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Affiliation(s)
- Cristian Obiol-Pardo
- Departamento de Química Física, Facultat de Química, Universitat de Barcelona and Institut de Recerca en Química Teòrica i Computacional (IQTCUB), Barcelona, Spain
| | - Gema Alcarraz-Vizán
- Departamento de Bioquímica i Biologia Molecular, Facultat de Biologia, Universitat de Barcelona and Institute of Biomedicine at Universitat de Barcelona (IBUB), Barcelona, Spain
| | - Marta Cascante
- Departamento de Bioquímica i Biologia Molecular, Facultat de Biologia, Universitat de Barcelona and Institute of Biomedicine at Universitat de Barcelona (IBUB), Barcelona, Spain
- * E-mail: (MC); (JRM)
| | - Jaime Rubio-Martinez
- Departamento de Química Física, Facultat de Química, Universitat de Barcelona and Institut de Recerca en Química Teòrica i Computacional (IQTCUB), Barcelona, Spain
- * E-mail: (MC); (JRM)
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Meshalkina LE, Solovjeva ON, Kochetov GA. Interaction of transketolase from human tissues with substrates. BIOCHEMISTRY (MOSCOW) 2012; 76:1061-4. [PMID: 22082276 DOI: 10.1134/s0006297911090112] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The Michaelis constant values for substrates of transketolase from human tissues were determined over a wide range of substrate concentrations. It is shown that K(m) values determined by other authors are significantly overestimated and explained why this is so.
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Affiliation(s)
- L E Meshalkina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Russia.
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Obiol-Pardo C, Cordero A, Rubio-Martinez J, Imperial S. Homology modeling of Mycobacterium tuberculosis 2C-methyl-D-erythritol-4-phosphate cytidylyltransferase, the third enzyme in the MEP pathway for isoprenoid biosynthesis. J Mol Model 2009; 16:1061-73. [PMID: 19916033 DOI: 10.1007/s00894-009-0615-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2009] [Accepted: 10/06/2009] [Indexed: 02/02/2023]
Abstract
Tuberculosis is one of the leading infectious diseases in humans. Discovering new treatments for this disease is urgently required, especially in view of the emergence of multiple drug resistant organisms and to reduce the total duration of current treatments. The synthesis of isoprenoids in Mycobacterium tuberculosis has been reported as an interesting pathway to target, and particular attention has been focused on the methylerythritol phosphate (MEP) pathway comprising the early steps of isoprenoid biosynthesis. In this context we have studied the enzyme 2C-methyl-D-erythritol-4-phosphate cytidylyltransferase (CMS), the third enzyme in the MEP pathway, since the lack of a resolved structure of this protein in M. tuberculosis has seriously limited its use as a drug target. We performed homology modeling of M. tuberculosis CMS in order to provide a reliable model for use in structure-based drug design. After evaluating the quality of the model, we performed a thorough study of the catalytic site and the dimerization interface of the model, which suggested the most important sites (conserved and non-conserved) that could be useful for drug discovery and mutagenesis studies. We found that the metal coordination of CDP-methylerythritol in M. tuberculosis CMS differs substantially with respect to the Escherichia coli variant, consistent with the fact that the former is able to utilize several metal ions for catalysis. Moreover, we propose that electrostatic interactions could explain the higher affinity of the MEP substrate compared with the cytosine 5'-triphosphate substrate in the M. tuberculosis enzyme as reported previously.
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Affiliation(s)
- Cristian Obiol-Pardo
- Dept. de Química Física, Universitat de Barcelona, Intitut de Recerca en Química Teòrica i Computacional (IQTCUB), Martí i Franquès 1, 08028, Barcelona, Spain
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