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Ricci A, Polverini E, Bruno S, Dramis L, Ceresini D, Scarano A, Diaz-Sala C. New Insights into the Enhancement of Adventitious Root Formation Using N,N'-Bis(2,3-methylenedioxyphenyl)urea. PLANTS (BASEL, SWITZERLAND) 2023; 12:3610. [PMID: 37896073 PMCID: PMC10610038 DOI: 10.3390/plants12203610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 10/11/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023]
Abstract
Adventitious rooting is a process of postembryonic organogenesis strongly affected by endogenous and exogenous factors. Although adventitious rooting has been exploited in vegetative propagation programs for many plant species, it is a bottleneck for vegetative multiplication of difficult-to-root species, such as many woody species. The purpose of this research was to understand how N,N'-bis-(2,3-methylenedioxyphenyl)urea could exert its already reported adventitious rooting adjuvant activity, starting from the widely accepted knowledge that adventitious rooting is a hormonally tuned progressive process. Here, by using specific in vitro bioassays, histological analyses, molecular docking simulations and in vitro enzymatic bioassays, we have demonstrated that this urea derivative does not interfere with polar auxin transport; it inhibits cytokinin oxidase/dehydrogenase (CKX); and, possibly, it interacts with the apoplastic portion of the auxin receptor ABP1. As a consequence of this dual binding capacity, the lifespan of endogenous cytokinins could be locally increased and, at the same time, auxin signaling could be favored. This combination of effects could lead to a cell fate transition, which, in turn, could result in increased adventitious rooting.
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Affiliation(s)
- Ada Ricci
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy
| | - Eugenia Polverini
- Dipartimento di Scienze Matematiche, Fisiche e Informatiche, Università di Parma, Parco Area delle Scienze 7/A, 43124 Parma, Italy
| | - Stefano Bruno
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università di Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Lucia Dramis
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy
| | - Daniela Ceresini
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy
| | - Antonio Scarano
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università di Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Carmen Diaz-Sala
- Departamento de Ciencias de la Vida, Universidad de Alcalá, 28871 Alcalá de Henares, Spain
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Kalyuta EV, Maltsev MI, Markin VI, Mashkina EI. Effect of Biopreparations Obtained from Carboxymethylated Plant Raw Material on the Wheat Growth, Crop Capacity, and Biochemical Parameters of Grain. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2022. [DOI: 10.1134/s1068162022070081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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3
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Sharifi Alishah M, Darvishzadeh R, Ahmadabadi M, Piri Kashtiban Y, Hasanpur K. Identification of differentially expressed genes in salt-tolerant oilseed sunflower (Helianthus annuus L.) genotype by RNA sequencing. Mol Biol Rep 2022; 49:3583-3596. [PMID: 35119610 DOI: 10.1007/s11033-022-07198-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/26/2022] [Indexed: 11/29/2022]
Abstract
BACKGROUND Sunflower (Helianthus annuus L.) is widely planted as an oilseed crop worldwide. Salt stress is one of the major abiotic stresses that negatively affect crop growth and productivity. To counter the negative impact of salt stress, plants have developed avoidance and tolerance mechanisms. Developing salt-tolerant genotypes requires understanding the molecular basis of adaptive mechanisms in depth. Although using model plants i.e., Arabidopsis has improved our understanding of salt tolerant mechanisms, the relative impotence and regulation mechanisms vary among plant species due to differences in genetic and metabolic backgrounds. On the other hand, sunflower is a highly polymorphic plant due to its cross-pollinated behavior which provides different salt-tolerant genotypes available for comparative analyses. METHODS AND RESULTS In order to gain a better view of molecular mechanisms involved in salt tolerance in sunflower, RNA sequencing analysis was realized by evaluating a tolerant genotype (AS5305) with two biological replicates under control and salt stress conditions in a controlled environment. Salinity stress was applied from NaCl resource at the 8-leaf stage and samplings were done at 24 h post salt stress application. Sequencing data were analyzed using tuxedo software suite. Blast2GO software and the KEGG database were used to identify the functional tasks of each of the assembled transcripts. Analysis of genes with robust expression (i.e., with FPKM > 1 in at least one sample) revealed a total of 121 significantly expressed genes between the saline-stressed and control samples. The differential expression of 11 genes was confirmed by real-time PCR. In the following, the cDNA of MYB44 as one of the selected candidate genes involved in salt tolerance was isolated, cloned, and sequenced for comparison. CONCLUSIONS Overall, the results of the current study may pave the way for the accurate selection of genes involved in salinity to be used in molecular-genetics-assisted breeding programs. In addition, making use of the identified genes may help relieve the damages arising from the salt stress in sunflowers.
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Affiliation(s)
- Masoumeh Sharifi Alishah
- Department of Plant Production and Genetics, Faculty of Agriculture, Urmia University, Urmia, Iran
| | - Reza Darvishzadeh
- Department of Plant Production and Genetics, Faculty of Agriculture, Urmia University, Urmia, Iran. .,Department of Agricultural Biotechnology, Institute of Biotechnology, Urmia University, Urmia, Iran.
| | - Mohammad Ahmadabadi
- Department Agricultural Biotechnology, Faculty of Agriculture, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Yaser Piri Kashtiban
- Department of Agricultural Biotechnology, National Center of Genetic Engineering, Tehran, Iran
| | - Karim Hasanpur
- Department of Animal Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
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Abstract
The auxin-binding protein 1 (ABP1) has endured a history of undulating prominence as a candidate receptor for this important phytohormone. Its capacity for binding auxin has not been in doubt, a feature adequately explained by its crystal structure, but any relevance of this to auxin signaling and plant development has been far more demanding to define. Over its research lifetime, it has been associated with many auxin-induced activities, including ion fluxes across the plasma membrane, rearrangement of the cytoskeleton and cell shape, and the abundance of PIN proteins at the plasma membrane via control of endocytosis, all of which required its presence in the apoplast. Yet, ABP1 has a KDEL sequence that targets it to the endoplasmic reticulum, where most of it remains. This mismatch has been more than adequately compensated for by the need for an auxin receptor to account for responses far too rapid to be executed through transcription and translation and the TIR1/AuxIAA coreceptor system. However, discoveries showing that abp1-null mutants are not compromised for auxin signaling or development, that TIR1 or AFB1 are necessarily involved with very rapid responses at the plasma membrane, and that these rapid responses are mediated with intracellular auxin all suggest that ABP1's auxin-binding capacity is not physiologically relevant. Nevertheless, ABP1 is ubiquitous in higher plants and throughout plant tissues. We need to complete its history by defining its function inside plant cells.
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Affiliation(s)
- Richard Napier
- School of Life Sciences, University of Warwick, Coventry CV4 7AS, United Kingdom
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5
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Comparison of tolerance related proteomic profiles of two drought tolerant tomato mutants improved by gamma radiation. J Biotechnol 2021; 330:35-44. [PMID: 33652074 DOI: 10.1016/j.jbiotec.2021.02.012] [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: 09/09/2020] [Revised: 01/30/2021] [Accepted: 02/23/2021] [Indexed: 11/23/2022]
Abstract
Lycopersicon esculentum L., also known as tomato, is an important industrial plant due to its products which worth billions of dollars annually, besides its nutritional value and health benefits. In this study, we investigated the two-dimensional protein expression profiles in drought tolerant mutant plants derived from industrial 5MX12956 tomato variety by Cs-137 gamma radiation source induced mutations. Drought tolerance of mutants were evaluated and confirmed by in vivo and in vitro methods. Eleven drought responsive protein spots were identified by two-dimensional electrophoresis and MALDI-TOF-MS. Identified proteins which presented differential expression under drought conditions were clustered under six distinct groups based on their cellular functions. These clusters are ATP and carbohydrate metabolism, mRNA processing and protein phosphorylation, oxidation reduction and stress response, signaling and supporting cytoskeleton. Our results contributed proteomic data to drought tolerance of our tomato mutants which were originated from drought susceptible 5MX12956 variety. They may also facilitate basis for future investigations into the genetic and physiological aspects of this tolerance.
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Dhar YV, Lakhwani D, Pandey A, Singh S, Trivedi PK, Asif MH. Genome-wide identification and interactome analysis of members of two-component system in Banana. BMC Genomics 2019; 20:674. [PMID: 31455217 PMCID: PMC6712864 DOI: 10.1186/s12864-019-6050-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Accepted: 08/20/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Ethylene signal transduction in plants is conducted by the two-component system (TCS) which consists of histidine kinase (HK), histidine phosphotransferase (HPT) and response regulators (RRs). This system plays an important role in signal transduction during various cellular processes, including fruit ripening and response to multiple environmental cues. Though members of TCS have been identified in a few plants, no detailed analysis has been carried out in banana. RESULTS Through genome-wide analysis, we identified a total of 80 (25 HK, 10 HPT and 45 RR) and 72 (25 HK, 5 HPT and 42 RR) TCS genes in Musa acuminata and Musa balbisiana respectively. The analysis of identified genes revealed that most of the genes are highly conserved however; there are subtle divergences among various members. Comparative expression analysis revealed an involvement of a set of TCS members during banana fruit ripening. Co-expression network analysis identified a working TCS module with direct interactions of HK-HPT and RR members. The molecular dynamics analysis of TCS module showed a significant change in structural trajectories of TCS proteins in the presence of ethylene. Analysis suggests possible interactions between the HK-HPTs and RRs as well as other members leading to banana fruit ripening. CONCLUSIONS In this study, we identified and compared the members of TCS gene family in two banana species and showed their diversity, within groups on the basis of whole-genome duplication events. Our analysis showed that during banana fruit ripening TCS module plays a crucial role. We also demonstrated a possible interaction mechanism of TCS proteins in the presence and absence of ethylene by molecular dynamics simulations. These findings will help in understanding the functional mechanism of TCS proteins in plants in different conditions.
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Affiliation(s)
- Yogeshwar V Dhar
- CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Deepika Lakhwani
- CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Ashutosh Pandey
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, P.O. Box No. 10531, New Delhi, 110 067, India
| | - Shikha Singh
- CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India
| | - Prabodh K Trivedi
- CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
| | - Mehar H Asif
- CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Tomić A, Horvat G, Ramek M, Agić D, Brkić H, Tomić S. New Zinc Ion Parameters Suitable for Classical MD Simulations of Zinc Metallopeptidases. J Chem Inf Model 2019; 59:3437-3453. [PMID: 31274304 DOI: 10.1021/acs.jcim.9b00235] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The main aim of this work was to find parameters for the zinc ion in human dipeptidyl peptidase III (DPP III) active site that would enable its reliable modeling. Since the parameters publicly available failed to reproduce the zinc ion coordination in the enzyme, we developed a new set of the hybrid bonded/nonbonded parameters for the zinc ion suitable for molecular modeling of the human DPP III, dynamics, and ligand binding. The parameters allowed exchange of the water molecules coordinating the zinc ion and proved to be robust enough to enable reliable modeling not only of human DPP III and its orthologues but also of the other zinc-dependent peptidases with the zinc ion coordination similar to that in dipeptidyl peptidases III, i.e., peptidases with the zinc ion coordinated with two histidines and one glutamate. The new parameters were tested on a set of 21 different systems comprising 8 different peptidases, 5 DPP III orthologues, thermolysin, neprilysin, and aminopeptidase N, and the results are summarized in the second part of the article.
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Affiliation(s)
- Antonija Tomić
- Division of Organic Chemistry and Biochemistry , Ruđer Bošković Institute , Bijenička 54 , 10 000 Zagreb , Croatia.,Institute of Physical and Theoretical Chemistry , Graz University of Technology , Stremayrgasse 9 , 8010 Graz , Austria
| | - Gordan Horvat
- Department of Chemistry, Faculty of Science , University of Zagreb , Horvatovac 102A , 10 000 Zagreb , Croatia
| | - Michael Ramek
- Institute of Physical and Theoretical Chemistry , Graz University of Technology , Stremayrgasse 9 , 8010 Graz , Austria
| | - Dejan Agić
- Faculty of Agrobiotechnical Sciences Osijek , Josip Juraj Strossmayer University of Osijek , Petra Svačića 1d , 31 000 Osijek , Croatia
| | - Hrvoje Brkić
- Faculty of Medicine , Josip Juraj Strossmayer University of Osijek , J. Huttlera 4 , 31 000 Osijek , Croatia.,Faculty of Dental Medicine and Health , Josip Juraj Strossmayer University of Osijek , Crkvena 21 , 31 000 Osijek , Croatia
| | - Sanja Tomić
- Division of Organic Chemistry and Biochemistry , Ruđer Bošković Institute , Bijenička 54 , 10 000 Zagreb , Croatia
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Tomin M, Tomić S. Oxidase or peptidase? A computational insight into a putative aflatoxin oxidase from Armillariella tabescens. Proteins 2019; 87:390-400. [PMID: 30681192 DOI: 10.1002/prot.25661] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 01/04/2019] [Accepted: 01/22/2019] [Indexed: 01/05/2023]
Abstract
Aflatoxin oxidase (AFO), an enzyme isolated from Armillariella tabescens, has been reported to degrade aflatoxin B1 (AFB1). However, recent studies reported sequence and structure similarities with the dipeptidyl peptidase III (DPP III) family of enzymes and confirmed peptidase activity toward DPP III substrates. In light of these investigations, an extensive computational study was performed in order to improve understanding of the AFO functions. Steered MD simulations revealed long-range domain motions described as protein opening, characteristic for DPPs III and necessary for substrate binding. Newly identified open and partially open forms of the enzyme closely resemble those of the human DPP III orthologue. Docking of a synthetic DPP III substrate Arg2 -2-naphthylamide revealed a binding mode similar to the one found in crystal structures of human DPP III complexes with peptides with the S1 and S2 subsites' amino acid residues conserved. On the other hand, no energetically favorable AFB1 binding mode was detected, suggesting that aflatoxins are not good substrates of AFO. High plasticity of the zinc ion coordination sphere within the active site, consistent with that of up to date studied DPPs III, was observed as well. A detailed electrostatic analysis of the active site revealed a predominance of negatively charged regions, unsuitable for the binding of the neutral AFB1. The present study is in line with the most recent experimental study on this enzyme, both suggesting that AFO is a typical member of the DPP III family.
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Affiliation(s)
- Marko Tomin
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Sanja Tomić
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
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9
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Sabljić I, Tomin M, Matovina M, Sučec I, Tomašić Paić A, Tomić A, Abramić M, Tomić S. The first dipeptidyl peptidase III from a thermophile: Structural basis for thermal stability and reduced activity. PLoS One 2018; 13:e0192488. [PMID: 29420664 PMCID: PMC5805324 DOI: 10.1371/journal.pone.0192488] [Citation(s) in RCA: 5] [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: 11/23/2017] [Accepted: 01/24/2018] [Indexed: 12/14/2022] Open
Abstract
Dipeptidyl peptidase III (DPP III) isolated from the thermophilic bacteria Caldithrix abyssi (Ca) is a two-domain zinc exopeptidase, a member of the M49 family. Like other DPPs III, it cleaves dipeptides from the N-terminus of its substrates but differently from human, yeast and Bacteroides thetaiotaomicron (mesophile) orthologs, it has the pentapeptide zinc binding motif (HEISH) in the active site instead of the hexapeptide (HEXXGH). The aim of our study was to investigate structure, dynamics and activity of CaDPP III, as well as to find possible differences with already characterized DPPs III from mesophiles, especially B. thetaiotaomicron. The enzyme structure was determined by X-ray diffraction, while stability and flexibility were investigated using MD simulations. Using molecular modeling approach we determined the way of ligands binding into the enzyme active site and identified the possible reasons for the decreased substrate specificity compared to other DPPs III. The obtained results gave us possible explanation for higher stability, as well as higher temperature optimum of CaDPP III. The structural features explaining its altered substrate specificity are also given. The possible structural and catalytic significance of the HEISH motive, unique to CaDPP III, was studied computationally, comparing the results of long MD simulations of the wild type enzyme with those obtained for the HEISGH mutant. This study presents the first structural and biochemical characterization of DPP III from a thermophile.
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Affiliation(s)
- Igor Sabljić
- Division of Physical Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Marko Tomin
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Mihaela Matovina
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Iva Sučec
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Ana Tomašić Paić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Antonija Tomić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Marija Abramić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Sanja Tomić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
- * E-mail:
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10
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da Costa CT, Pedebos C, Verli H, Fett-Neto AG. The role of Zn2+, dimerization and N-glycosylation in the interaction of Auxin-Binding Protein 1 (ABP1) with different auxins. Glycobiology 2017; 27:1109-1119. [DOI: 10.1093/glycob/cwx080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 09/04/2017] [Indexed: 01/12/2023] Open
Affiliation(s)
- Cibele Tesser da Costa
- Center for Biotechnology, Federal University of Rio Grande do Sul (UFRGS), CP 15005, Porto Alegre, RS 91501-970, Brazil
| | - Conrado Pedebos
- Center for Biotechnology, Federal University of Rio Grande do Sul (UFRGS), CP 15005, Porto Alegre, RS 91501-970, Brazil
| | - Hugo Verli
- Center for Biotechnology, Federal University of Rio Grande do Sul (UFRGS), CP 15005, Porto Alegre, RS 91501-970, Brazil
| | - Arthur Germano Fett-Neto
- Center for Biotechnology, Federal University of Rio Grande do Sul (UFRGS), CP 15005, Porto Alegre, RS 91501-970, Brazil
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11
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Priya R, Sneha P, Rivera Madrid R, Doss CP, Singh P, Siva R. Molecular Modeling and Dynamic Simulation of Arabidopsis Thaliana
Carotenoid Cleavage Dioxygenase Gene: A Comparison with Bixa orellana
and Crocus Sativus. J Cell Biochem 2017; 118:2712-2721. [DOI: 10.1002/jcb.25919] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 01/30/2017] [Indexed: 01/18/2023]
Affiliation(s)
- R. Priya
- School of Bio Sciences and Technology; VIT University; Vellore 632014 Tamil Nadu India
| | - P. Sneha
- School of Bio Sciences and Technology; VIT University; Vellore 632014 Tamil Nadu India
| | - Renata Rivera Madrid
- Cenro de Investigacion Cientifica de Yucatan A.C. Calle 43 No. 130; Col. Chuburnade Hidalgo; Merida 97200 Yucatan Mexico
| | - C.George Priya Doss
- School of Bio Sciences and Technology; VIT University; Vellore 632014 Tamil Nadu India
| | - Pooja Singh
- Centre for Research in Biotechnology for Agriculture; University of Malaya; Kuala Lumpur 50603 Malaysia
| | - Ramamoorthy Siva
- School of Bio Sciences and Technology; VIT University; Vellore 632014 Tamil Nadu India
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12
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Tomin M, Tomić S. Dynamic properties of dipeptidyl peptidase III from Bacteroides thetaiotaomicron and the structural basis for its substrate specificity – a computational study. MOLECULAR BIOSYSTEMS 2017; 13:2407-2417. [PMID: 28971197 DOI: 10.1039/c7mb00310b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Dynamics and enzyme activity of dipeptidyl peptidase III, wild type and mutants, from the human gut symbiont Bacteroides thetaiotaomicron.
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Affiliation(s)
- M. Tomin
- Division of Organic Chemistry and Biochemistry
- Rudjer Boskovic Institute
- Croatia
| | - S. Tomić
- Division of Organic Chemistry and Biochemistry
- Rudjer Boskovic Institute
- Croatia
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13
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Agić D, Brkić H, Tomić S, Karačić Z, Špoljarević M, Lisjak M, Bešlo D, Abramić M. Validation of flavonoids as potential dipeptidyl peptidase III inhibitors: Experimental and computational approach. Chem Biol Drug Des 2016; 89:619-627. [DOI: 10.1111/cbdd.12887] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 09/05/2016] [Accepted: 10/08/2016] [Indexed: 10/20/2022]
Affiliation(s)
- Dejan Agić
- Faculty of Agriculture in Osijek; Josip Juraj Strossmayer University of Osijek; Osijek Croatia
| | - Hrvoje Brkić
- Faculty of Medicine; Josip Juraj Strossmayer University of Osijek; Osijek Croatia
| | | | | | - Marija Špoljarević
- Faculty of Agriculture in Osijek; Josip Juraj Strossmayer University of Osijek; Osijek Croatia
| | - Miroslav Lisjak
- Faculty of Agriculture in Osijek; Josip Juraj Strossmayer University of Osijek; Osijek Croatia
| | - Drago Bešlo
- Faculty of Agriculture in Osijek; Josip Juraj Strossmayer University of Osijek; Osijek Croatia
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14
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Tomić A, Berynskyy M, Wade RC, Tomić S. Molecular simulations reveal that the long range fluctuations of human DPP III change upon ligand binding. MOLECULAR BIOSYSTEMS 2016; 11:3068-80. [PMID: 26334575 DOI: 10.1039/c5mb00465a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The experimentally determined structures of human dipeptidyl peptidase III (DPP III) for the wild-type protein and for the complex of its E451A mutant with the peptide substrate, tynorphin, differ significantly in their overall shape. The two domains of the enzyme are separated by a wide cleft in the structure of the ligand-free enzyme, while in the ligand-bound mutant they are very close to each other, and the protein structure is extremely compact. Here, we applied a range of molecular dynamics simulation techniques to investigate the DPP III conformational landscape and the influence of ligand binding on the protein structure and dynamics. We used conventional, accelerated and steered methods to simulate DPP III and its complexes with tynorphin and with the preferred, synthetic, substrate Arg-Arg-2-naphthylamide. We found that DPP III can adopt a number of different forms in solution. The compact forms are more stable, but the open and partially closed states, spanning a wide range of conformations, can more effectively recognize the substrate which preferentially binds to the five-stranded β-core of the lower DPP III domain. The simulations indicated the existence of a dynamic equilibrium between open and semi-closed states and revealed two ways that the protein can close, leading to two distinct compact structures. The way in which the protein closes depends on the presence of the ligand.
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Affiliation(s)
- A Tomić
- Department of Physical Chemistry, Rudjer Boskovic Institute, Bijenička cesta 54, 10000, Zagreb, Croatia.
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15
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Matić J, Šupljika F, Tir N, Piotrowski P, Schmuck C, Abramić M, Piantanida I, Tomić S. Guanidiniocarbonyl-pyrrole-aryl conjugates as inhibitors of human dipeptidyl peptidase III: combined experimental and computational study. RSC Adv 2016. [DOI: 10.1039/c6ra16966j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Good overlap of the standard DPP III substrate Arg-Arg-2NA (magenta) and the most efficient novel inhibitor (guanidiniocarbonyl-pyrrole-pyrene conjugate, blue-red) in the DPP III binding site.
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Affiliation(s)
- Josipa Matić
- Division of Organic Chemistry and Biochemistry
- Ruđer Bošković Institute
- 10000 Zagreb
- Croatia
| | - Filip Šupljika
- Division of Organic Chemistry and Biochemistry
- Ruđer Bošković Institute
- 10000 Zagreb
- Croatia
| | - Nora Tir
- Division of Organic Chemistry and Biochemistry
- Ruđer Bošković Institute
- 10000 Zagreb
- Croatia
| | - Patryciusz Piotrowski
- Institute for Organic Chemistry
- University of Duisburg-Essen
- Universitässtrasse 7
- 45141 Essen
- Germany
| | - Carsten Schmuck
- Institute for Organic Chemistry
- University of Duisburg-Essen
- Universitässtrasse 7
- 45141 Essen
- Germany
| | - Marija Abramić
- Division of Organic Chemistry and Biochemistry
- Ruđer Bošković Institute
- 10000 Zagreb
- Croatia
| | - Ivo Piantanida
- Division of Organic Chemistry and Biochemistry
- Ruđer Bošković Institute
- 10000 Zagreb
- Croatia
| | - Sanja Tomić
- Division of Organic Chemistry and Biochemistry
- Ruđer Bošković Institute
- 10000 Zagreb
- Croatia
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Characteristics of the influence of auxins on physicochemical properties of membrane phospholipids in monolayers at the air/aqueous solution interface. Colloids Surf B Biointerfaces 2015; 136:1131-8. [DOI: 10.1016/j.colsurfb.2015.11.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 11/09/2015] [Accepted: 11/11/2015] [Indexed: 11/21/2022]
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17
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Feng M, Kim JY. Revisiting Apoplastic Auxin Signaling Mediated by AUXIN BINDING PROTEIN 1. Mol Cells 2015; 38:829-35. [PMID: 26467289 PMCID: PMC4625063 DOI: 10.14348/molcells.2015.0205] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 10/04/2015] [Accepted: 10/05/2015] [Indexed: 02/04/2023] Open
Abstract
It has been suggested that AUXIN BINDING PROTEIN 1 (ABP1) functions as an apoplastic auxin receptor, and is known to be involved in the post-transcriptional process, and largely independent of the already well-known SKP-cullin-F-box-transport inhibitor response (TIR1) /auxin signaling F-box (AFB) (SCF(TIR1/AFB)) pathway. In the past 10 years, several key components downstream of ABP1 have been reported. After perceiving the auxin signal, ABP1 interacts, directly or indirectly, with plasma membrane (PM)-localized transmembrane proteins, transmembrane kinase (TMK) or SPIKE1 (SPK1), or other unidentified proteins, which transfer the signal into the cell to the Rho of plants (ROP). ROPs interact with their effectors, such as the ROP interactive CRIB motif-containing protein (RIC), to regulate the endocytosis/exocytosis of the auxin efflux carrier PIN-FORMED (PIN) proteins to mediate polar auxin transport across the PM. Additionally, ABP1 is a negative regulator of the traditional SCF(TIR1/AFB) auxin signaling pathway. However, Gao et al. (2015) very recently reported that ABP1 is not a key component in auxin signaling, and the famous abp1-1 and abp1-5 mutant Arabidopsis lines are being called into question because of possible additional mutantion sites, making it necessary to reevaluate ABP1. In this review, we will provide a brief overview of the history of ABP1 research.
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Affiliation(s)
- Mingxiao Feng
- Division of Applied Life Science (BK21plus program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701,
Korea
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21plus program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701,
Korea
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18
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Tomić A, Tomić S. Hunting the human DPP III active conformation: combined thermodynamic and QM/MM calculations. Dalton Trans 2015; 43:15503-14. [PMID: 25192149 DOI: 10.1039/c4dt02003k] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Multiple choices of the protein active conformations in flexible metalloenzymes complicate study of their catalytic mechanism. We used three different conformations of human dipeptidyl-peptidase III (DPP III) to investigate the influence of the protein environment on ligand binding and the Zn(2+) coordination. MD simulations followed by calculations of binding free energy components accomplished for a series of DPP III substrates, both synthetic and natural, revealed that binding of the β-strand shaped substrate to the five-stranded β-core of the compact DPP III form (in antiparallel fashion) is the preferred binding mode, in agreement with the experimentally determined structure of the DPP III inactive mutant-tynorphin complex (Bezerra et al., Proc. Natl. Acad. Sci. U. S. A., 2012, 109, 6525). Previously it was proposed that the catalytic mechanism of DPP III is similar to that of thermolysin, which assumes exchange of five and four coordinated Zn(2+), and activation of Zn-bound water by a nearby Glu. Our QM/MM calculations, performed for a total of 18 protein structures with different zinc ion environments, revealed that the 5-coordinated metal ion is more favourable than the 6-coordinated one in only the most compact DPP III form. Besides, in this structure E451 is H-bonded to the metal ion coordinating water. Also, our study revealed two constraints for the broad substrate specificity of DPP III. One is the possibility of the substrate adopting the β-strand shape and the other is its charged N-terminus. Altogether, we assume that the human DPP III active conformation would be the most compact form, similar to the "closed X-ray" DPP III structure.
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Affiliation(s)
- Antonija Tomić
- Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička 54, 10 000 Zagreb, Croatia.
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19
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Grandits M, Oostenbrink C. Molecular dynamics simulations of the auxin-binding protein 1 in complex with indole-3-acetic acid and naphthalen-1-acetic acid. Proteins 2014; 82:2744-55. [PMID: 25043515 DOI: 10.1002/prot.24639] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 06/20/2014] [Accepted: 06/30/2014] [Indexed: 11/08/2022]
Abstract
Auxin-binding protein 1 (ABP1) is suggested to be an auxin receptor which plays an important role in several processes in green plants. Maize ABP1 was simulated with the natural auxin indole-3-acetic acid (IAA) and the synthetic analog naphthalen-1-acetic acid (NAA), to elucidate the role of the KDEL sequence and the helix at the C-terminus. The KDEL sequence weakens the intermolecular interactions between the monomers but stabilizes the C-terminal helix. Conformational changes at the C-terminus occur within the KDEL sequence and are influenced by the binding of the simulated ligands. This observation helps to explain experimental findings on ABP1 interactions with antibodies that are modulated by the presence of auxin, and supports the hypothesis that ABP1 acts as an auxin receptor. Stable hydrogen bonds between the monomers are formed between Glu40 and Glu62, Arg10 and Thr97, Lys39, and Glu62 in all simulations. The amino acids Ile22, Leu25, Trp44, Pro55, Ile130, and Phe149 are located in the binding pocket and are involved in hydrophobic interactions with the ring system of the ligand. Trp151 is stably involved in a face to end interaction with the ligand. The calculated free energy of binding using the linear interaction energy approach showed a higher binding affinity for NAA as compared to IAA. Our simulations confirm the asymmetric behavior of the two monomers, the stronger interaction of NAA than IAA and offers insight into the possible mechanism of ABP1 as an auxin receptor.
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Affiliation(s)
- Melanie Grandits
- Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, A-1190, Vienna, Austria
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20
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Mládková J, Hladílková J, Diamond CE, Tryon K, Yamada K, Garrow TA, Jungwirth P, Koutmos M, Jiráček J. Specific potassium ion interactions facilitate homocysteine binding to betaine-homocysteine S
-methyltransferase. Proteins 2014; 82:2552-64. [DOI: 10.1002/prot.24619] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 05/24/2014] [Accepted: 05/28/2014] [Indexed: 12/17/2022]
Affiliation(s)
- Jana Mládková
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic; v.v.i., Flemingovo nám. 2, 166 10 Prague 6 Czech Republic
| | - Jana Hladílková
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic; v.v.i., Flemingovo nám. 2, 166 10 Prague 6 Czech Republic
| | - Carrie E. Diamond
- Department of Food Science and Human Nutrition; University of Illinois; Urbana Illinois 61801
| | - Katherine Tryon
- Department of Food Science and Human Nutrition; University of Illinois; Urbana Illinois 61801
| | - Kazuhiro Yamada
- Department of Biochemistry and Molecular Biology; Uniformed Services University of the Health Sciences; Bethesda Maryland 20814
| | - Timothy A. Garrow
- Department of Food Science and Human Nutrition; University of Illinois; Urbana Illinois 61801
| | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic; v.v.i., Flemingovo nám. 2, 166 10 Prague 6 Czech Republic
| | - Markos Koutmos
- Department of Biochemistry and Molecular Biology; Uniformed Services University of the Health Sciences; Bethesda Maryland 20814
| | - Jiří Jiráček
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic; v.v.i., Flemingovo nám. 2, 166 10 Prague 6 Czech Republic
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21
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Jajčanin-Jozić N, Tomić S, Abramić M. Importance of the three basic residues in the vicinity of the zinc-binding motifs for the activity of the yeast dipeptidyl peptidase III. ACTA ACUST UNITED AC 2013; 155:43-50. [DOI: 10.1093/jb/mvt093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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22
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Peer WA. From perception to attenuation: auxin signalling and responses. CURRENT OPINION IN PLANT BIOLOGY 2013; 16:561-8. [PMID: 24004572 DOI: 10.1016/j.pbi.2013.08.003] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 08/09/2013] [Accepted: 08/14/2013] [Indexed: 05/10/2023]
Abstract
The plant hormone auxin is essential for growth, development, and responses to environmental factors. Recently, Auxin Binding Protein 1 was shown to mediate non-transcriptional auxin signalling at the cell periphery. This has provoked reexamination of the paradigm that all auxin perception is intracellular and is mediated by the TIR1/AFB-Aux/IAA co-receptors for which auxin functions as a concentration-dependent molecular glue. Further, another F-box protein, SKP2a, was shown to bind auxin in the same way as TIR1/AFB, which provides a link to the role of auxin in the cell cycle. New work on auxin signalling and homeostasis include D6 PROTEIN KINASE activation of PINFORMED (PIN) auxin carriers, ROP-GTPase mediation of PIN localization, endoplasmic reticulum localization PIN and PIN-LIKES auxin carriers, and auxin biosynthesis and metabolism.
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Affiliation(s)
- Wendy Ann Peer
- Department of Environmental Science and Technology, University of Maryland, 5138 Plant Science Building, College Park, MD 20742, USA; Department of Plant Science and Landscape Architecture, University of Maryland, 5138 Plant Science Building, College Park, MD 20742, USA.
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23
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Hao GF, Yang SG, Yang GF, Zhan CG. Computational gibberellin-binding channel discovery unraveling the unexpected perception mechanism of hormone signal by gibberellin receptor. J Comput Chem 2013; 34:2055-64. [PMID: 23765254 DOI: 10.1002/jcc.23355] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 05/01/2013] [Accepted: 05/23/2013] [Indexed: 11/10/2022]
Abstract
Gibberellins (GAs) are phytohormones essential for many developmental processes in plants. In this work, fundamental mechanism of hormone perception by receptor GID1 has been studied by performing computational simulations, revealing a new GA-binding channel of GID1 and a novel hormone perception mechanism involving only one conformational state of GID1. The novel hormone perception mechanism demonstrated here is remarkably different from the previously proposed/speculated mechanism [Murase et al., Nature 2008, 456, 459] involving two conformational states ("OPEN" and "CLOSED") of GID1. According to the new perception mechanism, GA acts as a "conformational stabilizer," rather than the previously speculated "allosteric inducer," to induce the recognition of protein DELLA by GID1. The novel mechanistic insights obtained in this study provide a new starting point for further studies on the detailed molecular mechanisms of GID1 interacting with DELLA and various hormones and for mechanism-based rational design of novel, potent growth regulators that target crops and ornamental plants.
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Affiliation(s)
- Ge-Fei Hao
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, People's Republic of China
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24
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Abstract
Mechanisms governing dynamic protein recycling include small GTPases that activate/inactivate their partner proteins to affect cytoskeletal dynamics, and thereby polar growth, asymmetric cell shape and physiological responses to external stimuli. Three recent studies illustrate the control of PIN endocytosis by ROP-RIC activity in leaf pavement cells and root cells.
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25
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Pietra F. Putative binding sites, and pathways to them, for amidine and guanidine current inhibitors on acid-sensing ion channels (ASIC). A theoretical approach with hASIC1a homology model. Chem Biodivers 2012; 9:331-51. [PMID: 22344909 DOI: 10.1002/cbdv.201100260] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Central inhibition of the acid-sensing hASIC1a channel, acting upstream of the opiate system, might serve to treat any type of pain, avoiding the unwanted addiction problems of the opioid drugs. To this end, inhibition of hASIC1a channel by PcTx1, a peptide from the Trinidad chevron tarantula, is under development. New inhibitors of the hASIC1a channel are also being sought, in the hope of further modulating the activity, from which antiplasmodial amidine and guanidine phenyl drugs have emerged as promising candidates. However, how such current inhibition takes place remains obscure from the molecular point of view, hindering any further progress in developing drugs. Therefore, the nature of the binding sites, and how they are reached by the amidine-guanidine drugs, was investigated here via automated docking and molecular dynamics with hASIC1a homology models. This study has revealed that this ion channel is rich in binding sites, and that flexible drugs, such as nafamostat, may penetrate it in a snake-like elongated conformation. Then, crawling like a snake through temporary holes in the protein, nafamostat either simply flips, or changes to a high-energy folded conformation to become adapted to the shape of the binding site.
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Affiliation(s)
- Francesco Pietra
- Accademia Lucchese di Scienze, Lettere e Arti, Classe di Scienze, Palazzo Ducale, I-55100 Lucca, Italy.
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26
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Tomić A, González M, Tomić S. The large scale conformational change of the human DPP III-substrate prefers the "closed" form. J Chem Inf Model 2012; 52:1583-94. [PMID: 22656863 DOI: 10.1021/ci300141k] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Human dipeptidyl peptidase III (DPP III) is a two domain metallo-peptidase from the M49 family. The wide interdomain cleft and broad substrate specificity suggest that this enzyme could experience significant conformational change. Long (>100 ns) molecular dynamics (MD) simulations of DPP III revealed large range conformational changes of the protein, suggesting the pre-existing equilibrium model for a substrate binding. The binding free energy calculations revealed tighter binding of the preferred synthetic substrate Arg-Arg-2-naphtylamide to the "closed" than to the "open" DPP III conformation. Our assumption that Asp372 plays a crucial role in the large scale interdomain closure was proved by the MD simulations of the Asp372Ala variant. During the same simulation time, the variant remained more "open" than the wild type protein. Apparently, Ala was not as efficient as Asp in establishing the interdomain interactions. According to the MM-PBSA calculations, the electrostatic component of the free energy of solvation turned out to be higher for the "closed" protein than for its less compact form. However, the gain in entropy due to water released from the interdomain cleft nicely balanced this negative effect.
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Affiliation(s)
- Antonija Tomić
- Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička 54, 10 000 Zagreb, Croatia
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27
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Chromatography, mass spectrometry, and molecular modeling studies on ammodytoxins. Anal Bioanal Chem 2012; 402:2737-48. [DOI: 10.1007/s00216-012-5754-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Revised: 01/13/2012] [Accepted: 01/16/2012] [Indexed: 10/28/2022]
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28
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Tomić A, Abramić M, Spoljarić J, Agić D, Smith DM, Tomić S. Human dipeptidyl peptidase III: insights into ligand binding from a combined experimental and computational approach. J Mol Recognit 2012; 24:804-14. [PMID: 21812054 DOI: 10.1002/jmr.1115] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Human dipeptidyl peptidase III (DPP III) is a zinc-exopeptidase with implied roles in protein catabolism, pain modulation, and defense against oxidative stress. To understand the mode of ligand binding into its active site, we performed molecular modeling, site-directed mutagenesis, and biochemical analyses. Using the recently determined crystal structure of the human DPP III we built complexes between both, the wild-type (WT) protein and its mutant H568N with the preferred substrate Arg-Arg-2-naphthylamide (RRNA) and a competitive inhibitor Tyr-Phe-hydroxamate (Tyr-Phe-NHOH). The mutation of the conserved His568, structurally equivalent to catalytically important His231 in thermolysin, to Asn, resulted in a 1300-fold decrease of k(cat) for RRNA hydrolysis and in significantly lowered affinity for the inhibitor. Molecular dynamics simulations revealed the key protein-ligand interactions as well as the ligand-induced reorganization of the binding site and its partial closure. Simultaneously, the non-catalytic domain was observed to stretch and the opening at the wide side of the inter-domain cleft became enhanced. The driving force for these changes was the formation of the hydrogen bond between Asp372 and the bound ligand. The structural and dynamical differences, found for the ligand binding to the WT enzyme and the H568N mutant, and the calculated binding free energies, agree well with the measured affinities. On the basis of the obtained results we suggest a possible reaction mechanism. In addition, this work provides a foundation for further site-directed mutagenesis experiments, as well as for modeling the reaction itself.
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Affiliation(s)
- Antonija Tomić
- Division of Physical Chemistry, Rudjer Bošković Institute Bijenička 54,10002 Zagreb, Croatia
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29
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Effendi Y, Scherer GFE. Auxin binding-protein1 (ABP1), a receptor to regulate auxin transport and early auxin genes in an interlocking system with PIN proteins and the receptor TIR1. PLANT SIGNALING & BEHAVIOR 2011; 6:1101-3. [PMID: 21822062 PMCID: PMC3260702 DOI: 10.4161/psb.6.8.16403] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Compared to the past 10 years, a flurry of publications, reviews, and experimental papers on ABP1 appeared in the last couple of years. Certainly, the reason is that new methods and conceptual approaches appeared to tackle the questions posed by this enigmatic auxin-binding protein. Part of the enigma is the obvious central importance of ABP1, documented by the embryo-lethal property of the homozygous T-DNA insertion into this gene1. At the same time, this very property hindered progress in studying ABP1. Another delaying influence on ABP1 research was the fact that regulation of early auxin genes was fully explained by the mechanism provided by TRI1, the second auxin receptor2-4.
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Affiliation(s)
- Yunus Effendi
- Leibniz Universität Hannover, Institut für Zierpflanzenbau und Gehölzforschung, Abt Molekulare Ertragsphysiologie, Hannover, Germany
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30
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Scherer GFE. AUXIN-BINDING-PROTEIN1, the second auxin receptor: what is the significance of a two-receptor concept in plant signal transduction? JOURNAL OF EXPERIMENTAL BOTANY 2011; 62:3339-57. [PMID: 21733909 DOI: 10.1093/jxb/err033] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Since we are living in the 'age of transcription', awareness of aspects other than transcription in auxin signal transduction seems to have faded. One purpose of this review is to recall these other aspects. The focus will also be on the time scales of auxin responses and their potential or known dependence on either AUXIN BINDING PROTEIN 1 (ABP1) or on TRANSPORT-INHIBITOR-RESISTANT1 (TIR1) as a receptor. Furthermore, both direct and indirect evidence for the function of ABP1 as a receptor will be reviewed. Finally, the potential functions of a two-receptor system for auxin and similarities to other two-receptor signalling systems in plants will be discussed. It is suggested that such a functional arrangement is a property of plants which strengthens tissue autonomy and overcomes the lack of nerves or blood circulation which are responsible for rapid signal transport in animals.
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Affiliation(s)
- Günther F E Scherer
- Leibniz-Universität Hannover, Institute for Ornamental Plants and Wood Science, Section Molecular Developmental Physiology, Herrenhäuser Str. 2, D-30419 Hannover, Germany.
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31
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Hao GF, Yang GF. The role of Phe82 and Phe351 in auxin-induced substrate perception by TIR1 ubiquitin ligase: a novel insight from molecular dynamics simulations. PLoS One 2010; 5:e10742. [PMID: 20505777 PMCID: PMC2873998 DOI: 10.1371/journal.pone.0010742] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2010] [Accepted: 04/28/2010] [Indexed: 11/19/2022] Open
Abstract
It is well known that Auxin plays a key role in controlling many aspects of plant growth and development. Crystal structures of Transport inhibitor response 1 (TIR1), a true receptor of auxin, were very recently determined for TIR1 alone and in complexes with auxin and different synthetic analogues and an Auxin/Indole-3-Acetic Acid (Aux/IAA) substrate peptide. However, the dynamic conformational changes of the key residues of TIR1 that take place during the auxin and substrate perception by TIR1 and the detailed mechanism of these changes are still unclear. In the present study, various computational techniques were integrated to uncover the detailed molecular mechanism of the auxin and Aux/IAA perception process; these simulations included molecular dynamics (MD) simulations on complexes and the free enzyme, the molecular mechanics Poisson Boltzmann surface area (MM-PBSA) calculations, normal mode analysis, and hydrogen bond energy (HBE) calculations. The computational simulation results provided a reasonable explanation for the structure-activity relationships of auxin and its synthetic analogues in view of energy. In addition, a more detailed model for auxin and Aux/IAA perception was also proposed, indicating that Phe82 and Phe351 played a pivotal role in Aux/IAA perception. Upon auxin binding, Phe82 underwent conformational changes to accommodate the subsequent binding of Aux/IAA. As a result, auxin enhances the TIR1-Aux/IAA interactions by acting as a "molecular glue". Besides, Phe351 acts as a "fastener" to further improve the substrate binding. The structural and mechanistic insights obtained from the present study will provide valuable clues for the future design of promising auxin analogues.
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Affiliation(s)
- Ge-Fei Hao
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, People's Republic of China
| | - Guang-Fu Yang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, People's Republic of China
- * E-mail:
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32
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Shishova M, Lindberg S. A new perspective on auxin perception. JOURNAL OF PLANT PHYSIOLOGY 2010; 167:417-22. [PMID: 20176409 DOI: 10.1016/j.jplph.2009.12.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2009] [Revised: 12/17/2009] [Accepted: 12/17/2009] [Indexed: 05/08/2023]
Abstract
An important question in modern plant biology concerns the mechanisms of auxin perception. Despite the recently discovered soluble receptor, the F-box protein TIR1, there is no doubt that another type of signal perception exists, and is linked to the plasma membrane. Two models for the receptor have been suggested: either the receptor includes a protein kinase, or it is coupled with a G-protein. We propose a third model, acting through Ca(2+)-channels in the plasma membrane. The model is based on the revealed rapid auxin-induced reactions, including changes in the membrane potential, shifts in cytosol concentration of Ca(2+) and H(+) and modulation of cell sensitivity to hormones by the external Ca(2+) concentration. Detailed inhibitor analysis with both living cells and isolated plasma membranes show that auxin might directly stimulate Ca(2+) transport through the plasma membrane. A hypothetical scheme of auxin perception at the plasma membrane is suggested together with further transduction events. In addition, comparative analyses of auxin and serotonin perceptions are provided.
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Affiliation(s)
- Maria Shishova
- Department of Plant Physiology and Biochemistry, St. Petersburg State University, 199034 St. Petersburg, Russia.
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33
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Dahlke RI, Luethen H, Steffens B. ABP1: an auxin receptor for fast responses at the plasma membrane. PLANT SIGNALING & BEHAVIOR 2010; 5:1-3. [PMID: 20592799 PMCID: PMC2835948 DOI: 10.4161/psb.5.1.10306] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2009] [Accepted: 10/12/2009] [Indexed: 05/18/2023]
Abstract
Auxin-binding protein 1 (ABP1) is an auxin receptor for responses not primarily regulated by gene regulation. One fast response is protoplast swelling. By using immunological ABP1 tools we showed that the highly conserved box a is not alone important for auxin binding. Box c is another part of the auxin binding domain.1 Here we present a novel method to analyze auxin-induced, ABP1-mediated effects at the plasma membrane on single cell level in vivo. The fluorescence of FM4-64 in the plasma membrane is reduced by auxin and this response is mediated by ABP1. This method indicates a functional role of ABP1 at the plasma membrane.
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Affiliation(s)
- Renate I Dahlke
- Botanisches Institut und Botanischer Garten der Christian-Albrechts-Universität zu Kiel, Kiel, Germany.
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34
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Abstract
Plant hormones control most aspects of the plant life cycle by regulating genome expression. Expression of auxin-responsive genes involves interactions among auxin-responsive DNA sequence elements, transcription factors and trans-acting transcriptional repressors. Transcriptional output from these auxin signaling complexes is regulated by proteasome-mediated degradation that is triggered by interaction with auxin receptor-E3 ubiquitin ligases such SCF(TIR1). Auxin signaling components are conserved throughout land plant evolution and have proliferated and specialized to control specific developmental processes.
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Affiliation(s)
- Elisabeth J Chapman
- Division of Biology, University of California, San Diego, La Jolla, California 92093-0116, USA.
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35
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Dahlke RI, Lüthen H, Steffens B. The auxin-binding pocket of auxin-binding protein 1 comprises the highly conserved boxes a and c. PLANTA 2009; 230:917-924. [PMID: 19669789 DOI: 10.1007/s00425-009-0995-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2009] [Accepted: 07/17/2009] [Indexed: 05/28/2023]
Abstract
The auxin-binding protein 1 (ABP1) has already been proved to be an extracellular receptor of auxin in single cell systems. Protoplasts of maize coleoptiles respond to auxin with an increase in volume. The 2-naphthaleneacetic acid (2-NAA), an inactive auxin analog, acts as an anti-auxin in protoplast swelling, as it suppresses the effect of indole-3-acetic acid (IAA). Antibodies raised against box a of ABP1 induce protoplast swelling in the absence of auxin. This response is inhibited by pre-incubation with 2-NAA. The effect of 2-NAA on swelling induced by agonistic antibodies appears to depend on the binding characteristics of the antibody. ScFv12, an antibody directed against box a, box c and the C-terminal domain of ABP1 also exhibits auxin-agonist activity which is, however, not abolished by 2-NAA. Neither does 2-NAA affect the activity of the C-terminal peptide of ABP1, which is predicted to interact with putative binding proteins of ABP1. These results support the view that box a and box c of ABP1 are auxin-binding domains.
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Affiliation(s)
- Renate I Dahlke
- Botanisches Institut und Botanischer Garten der Christian-Albrechts-Universität zu Kiel, 24118 Kiel, Germany
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Abstract
Auxin is a plant growth regulator involved in diverse fundamental developmental responses. Much is now known about auxin transport, via influx and efflux carriers, and about auxin perception and its role in gene regulation. Many developmental processes are dependent on peaks of auxin concentration and, to date, attention has been directed at the role of polar auxin transport in generating and maintaining auxin gradients. However, surprisingly little attention has focussed on the role and significance of auxin biosynthesis, which should be expected to contribute to active auxin pools. Recent reports on the function of the YUCCA flavin monooxygenases and a tryptophan aminotransferase in Arabidopsis have caused us to look again at the importance of local biosynthesis in developmental processes. Many alternative and redundant pathways of auxin synthesis exist in many plants and it is emerging that they may function in response to environmental cues.
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Affiliation(s)
- John W Chandler
- Department of Developmental Biology, University of Cologne, Gyrhofstrasse 17, Cologne, Germany.
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