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Scott NJA, Prickett TCR, Charles CJ, Espiner EA, Richards AM, Rademaker MT. Haemodynamic, hormonal and renal actions of osteocrin in normal sheep. Exp Physiol 2024; 109:1305-1316. [PMID: 38890799 PMCID: PMC11291853 DOI: 10.1113/ep091826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 05/20/2024] [Indexed: 06/20/2024]
Abstract
Osteocrin (OSTN) is an endogenous protein sharing structural similarities with the natriuretic peptides [NPs; atrial (ANP), B-type (BNP) and C-type (CNP) NP], which are hormones known for their crucial role in maintaining pressure/volume homeostasis. Osteocrin competes with the NPs for binding to the receptor involved in their clearance (NPR-C). In the present study, having identified, for the first time, the major circulating form of OSTN in human and ovine plasma, we examined the integrated haemodynamic, endocrine and renal effects of vehicle-controlled incremental infusions of ovine proOSTN (83-133) and its metabolism in eight conscious normal sheep. Incremental i.v. doses of OSTN produced stepwise increases in circulating concentrations of the peptide, and its metabolic clearance rate was inversely proportional to the dose. Osteocrin increased plasma levels of ANP, BNP and CNP in a dose-dependent manner, together with concentrations of their intracellular second messenger, cGMP. Increases in plasma cGMP were associated with progressive reductions in arterial pressure and central venous pressure. Plasma cAMP, renin and aldosterone were unchanged. Despite significant increases in urinary cGMP levels, OSTN administration was not associated with natriuresis or diuresis in normal sheep. These results support OSTN as an endogenous ligand for NPR-C in regulating plasma concentrations of NPs and associated cGMP-mediated bioactivity. Collectively, our findings support a role for OSTN in maintaining cardiovascular homeostasis.
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Affiliation(s)
- Nicola J. A. Scott
- Department of Medicine, Christchurch Heart InstituteUniversity of Otago ChristchurchChristchurchNew Zealand
| | - Timothy C. R. Prickett
- Department of Medicine, Christchurch Heart InstituteUniversity of Otago ChristchurchChristchurchNew Zealand
| | - Christopher J. Charles
- Department of Medicine, Christchurch Heart InstituteUniversity of Otago ChristchurchChristchurchNew Zealand
| | - Eric A. Espiner
- Department of Medicine, Christchurch Heart InstituteUniversity of Otago ChristchurchChristchurchNew Zealand
| | - A. Mark Richards
- Department of Medicine, Christchurch Heart InstituteUniversity of Otago ChristchurchChristchurchNew Zealand
- Cardiovascular Research Institute, National University Health SystemsCentre for Translational MedicineSingaporeSingapore
| | - Miriam T. Rademaker
- Department of Medicine, Christchurch Heart InstituteUniversity of Otago ChristchurchChristchurchNew Zealand
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Nicolas J, Magli S, Rabbachin L, Sampaolesi S, Nicotra F, Russo L. 3D Extracellular Matrix Mimics: Fundamental Concepts and Role of Materials Chemistry to Influence Stem Cell Fate. Biomacromolecules 2020; 21:1968-1994. [PMID: 32227919 DOI: 10.1021/acs.biomac.0c00045] [Citation(s) in RCA: 272] [Impact Index Per Article: 68.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Synthetic 3D extracellular matrices (ECMs) find application in cell studies, regenerative medicine, and drug discovery. While cells cultured in a monolayer may exhibit unnatural behavior and develop very different phenotypes and genotypes than in vivo, great efforts in materials chemistry have been devoted to reproducing in vitro behavior in in vivo cell microenvironments. This requires fine-tuning the biochemical and structural actors in synthetic ECMs. This review will present the fundamentals of the ECM, cover the chemical and structural features of the scaffolds used to generate ECM mimics, discuss the nature of the signaling biomolecules required and exploited to generate bioresponsive cell microenvironments able to induce a specific cell fate, and highlight the synthetic strategies involved in creating functional 3D ECM mimics.
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Affiliation(s)
- Julien Nicolas
- Université Paris-Saclay, CNRS, Institut Galien Paris-Saclay, , 92296 Châtenay-Malabry, France
| | - Sofia Magli
- University of Milano-Bicocca, Department of Biotechnology and Biosciences, Piazza della Scienza 2, 20126 Milan, Italy
| | - Linda Rabbachin
- University of Milano-Bicocca, Department of Biotechnology and Biosciences, Piazza della Scienza 2, 20126 Milan, Italy
| | - Susanna Sampaolesi
- University of Milano-Bicocca, Department of Biotechnology and Biosciences, Piazza della Scienza 2, 20126 Milan, Italy
| | - Francesco Nicotra
- University of Milano-Bicocca, Department of Biotechnology and Biosciences, Piazza della Scienza 2, 20126 Milan, Italy
| | - Laura Russo
- University of Milano-Bicocca, Department of Biotechnology and Biosciences, Piazza della Scienza 2, 20126 Milan, Italy
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Cheng C, Liu H, Tan C, Tong D, Zhao Y, Liu X, Si W, Wang L, Liang L, Li J, Wang C, Chen Q, Du Y, Wang QK, Ren X. Mutation in NPPA causes atrial fibrillation by activating inflammation and cardiac fibrosis in a knock-in rat model. FASEB J 2019; 33:8878-8891. [PMID: 31034774 DOI: 10.1096/fj.201802455rrr] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Atrial fibrillation (AF) affects >30 million individuals worldwide. However, no genetic mutation from human patients with AF has been linked to inflammation. Here, we show that AF-associated human variant p.Ile138Thr in natriuretic peptide A (NPPA) encoding the atrial natriuretic peptide (ANP) causes inflammation, fibroblast activation, atrial fibrosis, and AF in knock-in (KI) rats. Variant p.Ile138Thr inhibits the interaction between ANP and its receptor natriuretic peptide receptor A and reduces intracellular cGMP levels. RNA sequencing and follow-up analyses showed that mutant ANP (mANP) activates multiple innate immunity pathways, including TNF-α, NF-κB, and IL-1β signaling. mANP induces differentiation of cardiac fibroblasts (CFs) to myofibroblasts and promotes CF proliferation and fibrosis. These results suggest that NPPA variant p.Ile138Thr causes AF by activating TNF-α, NF-κB, and IL-1β signaling, inflammation, and fibrosis. Multiple computational programs suggest that p.Ile138Thr is damaging or deleterious. Based on the 2015 American College of Medical Genetics and Genomics Standards and Guidelines, p.Ile138Thr can be classified as a likely pathogenic variant. Variant p.Ile138Thr was found only in Asian people in the Genome Aggregation Database and Exome Aggregation Consortium database at an averaged frequency of 0.026%. An estimated 1.15 million Asian people carry the variant and might be at risk of AF. The KI rats may provide an inflammation-based, genetic animal model for AF valuable for testing anti-inflammation or other therapies for AF.-Cheng, C., Liu, H., Tan, C., Tong, D., Zhao, Y., Liu, X., Si, W., Wang, L., Liang, L., Li, J., Wang, C., Chen, Q., Du, Y., Wang, Q. K., Ren, X. Mutation in NPPA causes atrial fibrillation by activating inflammation and cardiac fibrosis in a knock-in rat model.
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Affiliation(s)
- Chen Cheng
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, China
| | - Huixia Liu
- Department of Cardiology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Chengcheng Tan
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, China
| | - Doudou Tong
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, China
| | - Yongxuan Zhao
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, China
| | - Xia Liu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, China
| | - Wenxia Si
- Department of Basic Medicine, Medical College, Hubei Polytechnic University, Huangshi, China
| | - Linlin Wang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, China
| | - Lina Liang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, China
| | - Jia Li
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, China
| | - Chenghui Wang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, China
| | - Qiuyun Chen
- Department of Molecular Cardiology, Cleveland Clinic, Cleveland, Ohio, USA.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Cleveland, Ohio, USA
| | - Yimei Du
- Institute of Cardiovascular Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; and
| | - Qing K Wang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, China.,Department of Molecular Cardiology, Cleveland Clinic, Cleveland, Ohio, USA.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Cleveland, Ohio, USA.,Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Xiang Ren
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, China
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Khan S, Farooq U, Kurnikova M. Protein stability and dynamics influenced by ligands in extremophilic complexes - a molecular dynamics investigation. MOLECULAR BIOSYSTEMS 2018; 13:1874-1887. [PMID: 28737816 DOI: 10.1039/c7mb00210f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
In this study, we explore the structural and dynamic adaptations of the Tryptophan synthase α-subunit in a ligand bound state in psychrophilic, mesophilic and hyperthermophilic organisms at different temperatures by MD simulations. We quantify the global and local fluctuations in the 40 ns time scale by analyzing the root mean square deviation/fluctuations. The distinct behavior of the active site and loop 6 is observed with the elevation of temperature. Protein stability relies more on electrostatic interactions, and these interactions might be responsible for the stability of varying temperature evolved proteins. The paper also focuses on the effect of temperature on protein dynamics and stability governed by the distinct behavior of the ligand associated with its retention, binding and dissociation over the course of time. The integration of principle component analysis and a free energy landscape was useful in identifying the conformational space accessible to ligand bound homologues and how the presence of the ligand alters the conformational and dynamic properties of the protein.
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Affiliation(s)
- Sara Khan
- Department of Chemistry, COMSATS Institute of Information Technology, Abbottabad-22060, Pakistan.
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Xue Z, Wen H, Wang C, Zhai L, Cheng A, Kou X. CPe-III-S Metabolism in Vitro and in Vivo and Molecular Simulation of Its Metabolites Using a p53-R273H Mutant. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:7095-7103. [PMID: 27584867 DOI: 10.1021/acs.jafc.6b01996] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
It was previously found that CPe-III-S, synthesized according to the chickpea peptide CPe-III (RQSHFANAQP), exhibited an antiproliferative effect. The aim of this study was to investigate the antiproliferative mechanism of CPe-III-S. CPe-III-S was treated by pepsin and trypsin in a simulated gastrointestinal digestion environment as well as in an animal experiment. With HPLC-ESI-MS analysis, three peptide fragments of Ser-His, His-Phe, and Ala-Asn-Ala-Gln were identified. Ser-His was the only common product from both in vitro and in vivo environments. The specific bindings between three peptides and p53-R273H were performed by molecular docking, and the molecular dynamic simulation between Ser-His and p53-R273H revealed the stability of the binding complex. The binding free energy of the complex was -12.56 ± 1.03 kcal/mol with a reliable hydrogen bond between the ligand and Thr284 of p53. Ser-His may restore mutant p53-R273H activity or inhibit its binding with a downstream signal. This metabolite is a potential anticancer factor for suppressing cell proliferation.
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Affiliation(s)
- Zhaohui Xue
- School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072, People's Republic of China
| | - Haichao Wen
- School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072, People's Republic of China
| | - Cen Wang
- School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072, People's Republic of China
| | - Lijuan Zhai
- School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072, People's Republic of China
| | - Aiqing Cheng
- School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072, People's Republic of China
| | - Xiaohong Kou
- School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072, People's Republic of China
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Modeling psychiatric disorders: from genomic findings to cellular phenotypes. Mol Psychiatry 2016; 21:1167-79. [PMID: 27240529 PMCID: PMC4995546 DOI: 10.1038/mp.2016.89] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 04/20/2016] [Accepted: 04/21/2016] [Indexed: 12/15/2022]
Abstract
Major programs in psychiatric genetics have identified >150 risk loci for psychiatric disorders. These loci converge on a small number of functional pathways, which span conventional diagnostic criteria, suggesting a partly common biology underlying schizophrenia, autism and other psychiatric disorders. Nevertheless, the cellular phenotypes that capture the fundamental features of psychiatric disorders have not yet been determined. Recent advances in genetics and stem cell biology offer new prospects for cell-based modeling of psychiatric disorders. The advent of cell reprogramming and induced pluripotent stem cells (iPSC) provides an opportunity to translate genetic findings into patient-specific in vitro models. iPSC technology is less than a decade old but holds great promise for bridging the gaps between patients, genetics and biology. Despite many obvious advantages, iPSC studies still present multiple challenges. In this expert review, we critically review the challenges for modeling of psychiatric disorders, potential solutions and how iPSC technology can be used to develop an analytical framework for the evaluation and therapeutic manipulation of fundamental disease processes.
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Zhang S, Geng X, Zhao L, Li J, Tian F, Wang Y, Fan R, Feng N, Liu J, Cheng L, Pei J. Cardiovascular and renal effect of CNAAC: An innovatively designed natriuretic peptide. Eur J Pharmacol 2015; 761:180-8. [PMID: 25979857 DOI: 10.1016/j.ejphar.2015.05.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 04/28/2015] [Accepted: 05/01/2015] [Indexed: 12/19/2022]
Abstract
Natriuretic peptides (NPs) have natriuretic, diuretic and vasodilator effects. An innovative natriuretic peptide analogue called CNAAC (a new chimera peptide combining the C-terminus and ring of ANP with the N-terminus of CNP) was designed to determine whether it has any cardiovascular and renal effect. Abdominal aorta of rats were isolated and vascular ring perfusion was employed to compare the vasodilator effect and cGMP excretion effect of CNAAC with natural NPs. Urine volume and urine cGMP levels after intravenous injection of CNAAC and natural NPs were determined. Hemodynamic methods were employed to assess the effect of CNAAC and natural NPs on MAP. CNAAC relaxed abdominal aorta in a dose-dependent manner and was independent of endothelium. The vasodilating effect of CNAAC was significantly attenuated in the presence of NPR-A antibody, GC inhibitor, and KATP inhibitor and was abolished by PKG inhibitor. Abdominal aortic cGMP production increased after incubation with NPs. Urine volume, plasma cGMP, and urine cGMP increased and MAP decreased dramatically after intravenous injection of CNAAC. CNAAC has a potent vasodilating effect, probably by activating K(+) channels via NPR-A/sGC/cGMP pathway. Exogenous administration of CNAAC elicits diuretic and hypotensive effects.
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Affiliation(s)
- Shumiao Zhang
- Department of Physiology, National Key Discipline of Cell Biology, Fourth Military Medical University, No.169 West Changle Road, Xi'an, 710032 Shaanxi Province, People's Republic of China
| | - Xiao Geng
- Department of Physiology, National Key Discipline of Cell Biology, Fourth Military Medical University, No.169 West Changle Road, Xi'an, 710032 Shaanxi Province, People's Republic of China
| | - Lei Zhao
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, No. 17 West Changle Road, Xi'an, 710033 Shaanxi Province, People's Republic of China
| | - Juan Li
- Department of Physiology, National Key Discipline of Cell Biology, Fourth Military Medical University, No.169 West Changle Road, Xi'an, 710032 Shaanxi Province, People's Republic of China
| | - Fei Tian
- Department of Physiology, National Key Discipline of Cell Biology, Fourth Military Medical University, No.169 West Changle Road, Xi'an, 710032 Shaanxi Province, People's Republic of China
| | - Yuemin Wang
- Department of Physiology, National Key Discipline of Cell Biology, Fourth Military Medical University, No.169 West Changle Road, Xi'an, 710032 Shaanxi Province, People's Republic of China
| | - Rong Fan
- Department of Physiology, National Key Discipline of Cell Biology, Fourth Military Medical University, No.169 West Changle Road, Xi'an, 710032 Shaanxi Province, People's Republic of China
| | - Na Feng
- Department of Physiology, National Key Discipline of Cell Biology, Fourth Military Medical University, No.169 West Changle Road, Xi'an, 710032 Shaanxi Province, People's Republic of China
| | - Jincheng Liu
- Department of Cardiovascular Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, 710033 Shaanxi Province, China
| | - Liang Cheng
- Department of Cardiovascular Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, 710033 Shaanxi Province, China.
| | - Jianming Pei
- Department of Physiology, National Key Discipline of Cell Biology, Fourth Military Medical University, No.169 West Changle Road, Xi'an, 710032 Shaanxi Province, People's Republic of China.
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Pizzoni D, Mascini M, Lanzone V, Del Carlo M, Di Natale C, Compagnone D. Selection of peptide ligands for piezoelectric peptide based gas sensors arrays using a virtual screening approach. Biosens Bioelectron 2013; 52:247-54. [PMID: 24060973 DOI: 10.1016/j.bios.2013.08.044] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 08/12/2013] [Accepted: 08/22/2013] [Indexed: 01/11/2023]
Abstract
Virtual and experimental affinity binding properties of 5 different peptides (cysteinylglycine, glutathione, Cys-Ile-His-Asn-Pro, Cys-Ile-Gln-Pro-Val, Cys-Arg-Gln-Val-Phe) vs. 14 volatile compounds belonging to relevant chemical classes were evaluated. The peptides were selected in order to have a large variability in physicochemical characteristics (including length). In virtual screening a rapid and cost-effective computational methodology for predicting binding scores of small peptide receptors vs. volatile compounds is proposed. Flexibility was considered for both ligands and peptides and each peptide conformer was treated as a possible receptor, generating a dedicated box and then running a docking process vs. all possible conformers of the 14 volatile compounds. The 5 peptides were covalently bound to gold nanoparticles and deposited onto 20 MHz quartz crystal microbalances to realize gas sensors. Gas sensing confirmed that each of the peptide conferred to the gold nanoparticles a particular selectivity pattern able to discriminate the 14 volatile compounds. The largest response was obtained for the pentapeptides Cys-Ile-His-Asn-Pro and Cys-Ile-Gln-Pro-Val while low response was achieved for the dipeptide. The comparative study, carried using a two-tailed T test, demonstrated that virtual screening was able to predict reliably the sensing ability of the pentapeptides. The dipeptide receptor exhibited 29% of virtual-experimental matching vs. 71% of glutathione and up to 93% for the pentapeptides. This virtual screening approach was proved to be a promising tool in predicting the behaviour of sensors array for gas detection.
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Affiliation(s)
- Daniel Pizzoni
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, 64023 Teramo, Italy.
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Mascini M, Montesano C, Sergi M, Perez G, De Cicco M, Curini R, Compagnone D. Peptides trapping cocaine: docking simulation and experimental screening by solid phase extraction followed by liquid chromatography mass spectrometry in plasma samples. Anal Chim Acta 2013; 772:40-6. [DOI: 10.1016/j.aca.2013.02.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Revised: 02/15/2013] [Accepted: 02/19/2013] [Indexed: 11/29/2022]
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10
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Bini A, Mascini M, Mascini M, Turner APF. Selection of thrombin-binding aptamers by using computational approach for aptasensor application. Biosens Bioelectron 2011; 26:4411-6. [PMID: 21636260 DOI: 10.1016/j.bios.2011.04.053] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2011] [Revised: 04/21/2011] [Accepted: 04/28/2011] [Indexed: 10/18/2022]
Abstract
The possibility of introducing a computationally assisted method to study aptamer-protein interaction was evaluated with the aim of streamlining the screening and selection of new aptamers. Starting from information on the 15-mer (5'-GGTTGGTGTGGTTGG-3') thrombin binding aptamer (TBA), a library of mutated DNA sequences (994 elements) was generated and screened using shapegauss a shape-based scoring function from openeye software to generate computationally derived binding scores. The TBA and three other mutated oligonucleotides, selected on the basis of their binding score (best, medium, worst), were incorporated into surface plasmon resonance (SPR) biosensors. By reducing the ionic strength (binding buffer, 50 mM TrisHCl pH 7.4, 140 mM NaCl, 1mM MgCl₂, diluted 1:50) in order to match the simulated condition, the analytical performances of the four oligonucleotide sequences were compared using signal amplitude, sensitivity (slope), linearity (R²) and reproducibility (CVav %). The experimental results were in agreement with the simulation findings.
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Affiliation(s)
- Alessandra Bini
- Dipartimento di Chimica, Università degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
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Batista PR, de Souza Costa MG, Pascutti PG, Bisch PM, de Souza W. High temperatures enhance cooperative motions between CBM and catalytic domains of a thermostable cellulase: mechanism insights from essential dynamics. Phys Chem Chem Phys 2011; 13:13709-20. [DOI: 10.1039/c0cp02697b] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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12
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Theoretical studies on the interactions of XIAP-BIR3 domain with bicyclic and tricyclic core monovalent Smac mimetics. J Mol Graph Model 2010; 29:354-62. [PMID: 20980180 DOI: 10.1016/j.jmgm.2010.09.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Revised: 09/14/2010] [Accepted: 09/23/2010] [Indexed: 11/21/2022]
Abstract
X-linked IAP can bind caspase-9 and inhibit its activity. Mitochondrial protein Smac/DIABLO can also interact with XIAP and relieve the inhibition on caspase-9 to induce apoptosis. A series of artificial Smac mimetics have been used to mimic the Smac N-terminal tetrapeptide AVPI to bind to XIAP-BIR3, but these structural diverse mimetics exhibited distinct binding affinities. To get an insight into the binding nature and optimize the structures, molecular docking and dynamics simulations were used to study the binding of XIAP-BIR3 with three groups of Smac mimetics. The docking results reveal that these Smac mimetics anchored on the surface groove of XIAP-BIR3 and superimposed well with AVPI. The modifications on the seven-membered ring of bicyclic core segment do not strengthen the binding affinity, while a benzyl introduced to the five-membered ring is favorable to the binding. Molecular dynamics simulations on three typical systems show that these complexes are very stable. Hydrogen bonds between the bicyclic core segment and Thr308 play critical roles in maintaining the stability of complex. The binding free energies calculated by MM_PBSA method are consistent with the experimental results.
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