1
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Kumari M, Singh R, Subbarao N. Exploring the interaction mechanism between potential inhibitor and multi-target Mur enzymes of mycobacterium tuberculosis using molecular docking, molecular dynamics simulation, principal component analysis, free energy landscape, dynamic cross-correlation matrices, vector movements, and binding free energy calculation. J Biomol Struct Dyn 2022; 40:13497-13526. [PMID: 34662260 DOI: 10.1080/07391102.2021.1989040] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Multi-targeting enzyme approaches are considered to be the most significant in suppressing pathogen growth and disease control for MDR and XDR-resistant Mycobacterium tuberculosis. The multiple Mur enzymes involved in peptidoglycan biosynthesis play a key role in a cell's growth. Firstly, homology modeling was employed to construct the 3 D structure of the Mur enzymes. The computational approaches, including molecular docking and molecular dynamics simulations and MM-PBSA methods, were performed to explore the detailed interaction mechanism to evaluate the inhibitory activity against targeted proteins. The computational calculations revealed that the best-docked phytochemical compound (gallomyricitrin) inhibits the selected targets: Mur enzymes by forming stable hydrogen bonds. The analysis of RMSD, RMSF, Rg, PCA, DCCM, cross-correlation network, FEL, H-bond, and vector movement reveal that the docked complex of MurA, MurI, MurG, MurC, and MurE is more stable compared to MurB, MurF, MurD, and MurX docked complexes during MD simulations. Moreover, FEL exposed that gallomyricitrin stabilized to the minimum global energy of Mur Enzymes. The PCA, DCCM, and vector movements and binding free energy results provided further evidence for the stability of gallomyricitrin's interactions inside the binding sites by forming hydrogen bonds. The cross-correlation analysis reveals that Mur enzymes exhibit a positive and negative correlated motion between residues in different protein domains. The computational results contribute in several ways to our understanding of inhibition activity and provide a basic insight into the binding activity of gallomyricitrin as a multi-target drug for tuberculosis. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Madhulata Kumari
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Ruhar Singh
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Naidu Subbarao
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
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2
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Trang NM, Vinh LB, Thanh NV, Phong NV. Inhibition of PTP1B by isosinensetin, a polymethoxylated flavone isolated from trifoliate orange peel: kinetic studies, molecular docking, and molecular dynamics simulation. CHEMICAL PAPERS 2022. [DOI: 10.1007/s11696-022-02560-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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3
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PPDPF promotes lung adenocarcinoma progression via inhibiting apoptosis and NK cell-mediated cytotoxicity through STAT3. Oncogene 2022; 41:4244-4256. [PMID: 35906391 DOI: 10.1038/s41388-022-02418-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 07/07/2022] [Accepted: 07/13/2022] [Indexed: 11/08/2022]
Abstract
Lung cancer is the most common malignancy and the leading cause of cancer death worldwide, and lung adenocarcinoma (LUAD) is the most prevalent subtype. Considering the emergence of resistance to therapies, it is urgent to develop more effective therapies to improve the prognosis. Here we reported that pancreatic progenitor cell differentiation and proliferation factor (PPDPF) deficiency inhibited LUAD development both in vitro and in vivo. Mechanistically, PPDPF induces hyperactive STAT3 by interfering STAT3-PTPN1 interaction. Activated STAT3 promoted BMPR2 transcription, which further inhibited apoptosis. Moreover, PPDPF reduced NK cell infiltration and activation to develop an immunosuppressive microenvironment, which was also mediated by STAT3. Furthermore, we identified that the expression of PPDPF was positively correlated with the malignant features of LUAD, as well as BMPR2 and p-STAT3 level in clinical samples. Therefore, our study suggests that PPDPF positively regulates BMPR2 expression and facilitates immune escape via regulating STAT3 activity, providing a potential therapy target for LUAD.
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4
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Liu R, Sun Y, Berthelet J, Bui LC, Xu X, Viguier M, Dupret JM, Deshayes F, Rodrigues Lima F. Biochemical, Enzymatic, and Computational Characterization of Recurrent Somatic Mutations of the Human Protein Tyrosine Phosphatase PTP1B in Primary Mediastinal B Cell Lymphoma. Int J Mol Sci 2022; 23:ijms23137060. [PMID: 35806064 PMCID: PMC9266312 DOI: 10.3390/ijms23137060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/23/2022] [Accepted: 06/23/2022] [Indexed: 12/16/2022] Open
Abstract
Human protein tyrosine phosphatase 1B (PTP1B) is a ubiquitous non-receptor tyrosine phosphatase that serves as a major negative regulator of tyrosine phosphorylation cascades of metabolic and oncogenic importance such as the insulin, epidermal growth factor receptor (EGFR), and JAK/STAT pathways. Increasing evidence point to a key role of PTP1B-dependent signaling in cancer. Interestingly, genetic defects in PTP1B have been found in different human malignancies. Notably, recurrent somatic mutations and splice variants of PTP1B were identified in human B cell and Hodgkin lymphomas. In this work, we analyzed the molecular and functional levels of three PTP1B mutations identified in primary mediastinal B cell lymphoma (PMBCL) patients and located in the WPD-loop (V184D), P-loop (R221G), and Q-loop (G259V). Using biochemical, enzymatic, and molecular dynamics approaches, we show that these mutations lead to PTP1B mutants with extremely low intrinsic tyrosine phosphatase activity that display alterations in overall protein stability and in the flexibility of the active site loops of the enzyme. This is in agreement with the key role of the active site loop regions, which are preorganized to interact with the substrate and to enable catalysis. Our study provides molecular and enzymatic evidence for the loss of protein tyrosine phosphatase activity of PTP1B active-site loop mutants identified in human lymphoma.
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Affiliation(s)
- Rongxing Liu
- Université Paris Cité, CNRS, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France; (R.L.); (L.-C.B.); (M.V.); (J.-M.D.); (F.D.)
| | - Yujie Sun
- School of Medicine and Pharmacy, Ocean University of China, Qingdao 266071, China; (Y.S.); (X.X.)
| | - Jérémy Berthelet
- Université Paris Cité, CNRS, Centre d’Epigénétique et Destin Cellulaire, F-75013 Paris, France;
| | - Linh-Chi Bui
- Université Paris Cité, CNRS, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France; (R.L.); (L.-C.B.); (M.V.); (J.-M.D.); (F.D.)
| | - Ximing Xu
- School of Medicine and Pharmacy, Ocean University of China, Qingdao 266071, China; (Y.S.); (X.X.)
| | - Mireille Viguier
- Université Paris Cité, CNRS, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France; (R.L.); (L.-C.B.); (M.V.); (J.-M.D.); (F.D.)
| | - Jean-Marie Dupret
- Université Paris Cité, CNRS, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France; (R.L.); (L.-C.B.); (M.V.); (J.-M.D.); (F.D.)
| | - Frédérique Deshayes
- Université Paris Cité, CNRS, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France; (R.L.); (L.-C.B.); (M.V.); (J.-M.D.); (F.D.)
| | - Fernando Rodrigues Lima
- Université Paris Cité, CNRS, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France; (R.L.); (L.-C.B.); (M.V.); (J.-M.D.); (F.D.)
- Correspondence:
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5
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Archaeal Lipids Regulating the Trimeric Structure Dynamics of Bacteriorhodopsin for Efficient Proton Release and Uptake. Int J Mol Sci 2022; 23:ijms23136913. [PMID: 35805918 PMCID: PMC9278134 DOI: 10.3390/ijms23136913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/19/2022] [Accepted: 06/20/2022] [Indexed: 11/30/2022] Open
Abstract
S-TGA-1 and PGP-Me are native archaeal lipids associated with the bacteriorhodopsin (bR) trimer and contribute to protein stabilization and native dynamics for proton transfer. However, little is known about the underlying molecular mechanism of how these lipids regulate bR trimerization and efficient photocycling. Here, we explored the specific binding of S-TGA-1 and PGP-Me with the bR trimer and elucidated how specific interactions modulate the bR trimeric structure and proton release and uptake using long-term atomistic molecular dynamic simulations. Our results showed that S-TGA-1 and PGP-Me are essential for stabilizing the bR trimer and maintaining the coherent conformational dynamics necessary for proton transfer. The specific binding of S-TGA-1 with W80 and K129 regulates proton release on the extracellular surface by forming a “Glu-shared” model. The interaction of PGP-Me with K40 ensures proton uptake by accommodating the conformation of the helices to recruit enough water molecules on the cytoplasmic side. The present study results could fill in the theoretical gaps of studies on the functional role of archaeal lipids and could provide a reference for other membrane proteins containing similar archaeal lipids.
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Wilson CJ, Chang M, Karttunen M, Choy WY. KEAP1 Cancer Mutants: A Large-Scale Molecular Dynamics Study of Protein Stability. Int J Mol Sci 2021; 22:5408. [PMID: 34065616 PMCID: PMC8161161 DOI: 10.3390/ijms22105408] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 12/30/2022] Open
Abstract
We have performed 280 μs of unbiased molecular dynamics (MD) simulations to investigate the effects of 12 different cancer mutations on Kelch-like ECH-associated protein 1 (KEAP1) (G333C, G350S, G364C, G379D, R413L, R415G, A427V, G430C, R470C, R470H, R470S and G476R), one of the frequently mutated proteins in lung cancer. The aim was to provide structural insight into the effects of these mutants, including a new class of ANCHOR (additionally NRF2-complexed hypomorph) mutant variants. Our work provides additional insight into the structural dynamics of mutants that could not be analyzed experimentally, painting a more complete picture of their mutagenic effects. Notably, blade-wise analysis of the Kelch domain points to stability as a possible target of cancer in KEAP1. Interestingly, structural analysis of the R470C ANCHOR mutant, the most prevalent missense mutation in KEAP1, revealed no significant change in structural stability or NRF2 binding site dynamics, possibly indicating an covalent modification as this mutant's mode of action.
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Affiliation(s)
- Carter J. Wilson
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5C1, Canada; (C.J.W.); (M.C.)
- Department of Applied Mathematics, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5B7, Canada
| | - Megan Chang
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5C1, Canada; (C.J.W.); (M.C.)
| | - Mikko Karttunen
- Department of Applied Mathematics, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5B7, Canada
- Department of Chemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 3K7, Canada
- Centre for Advanced Materials and Biomaterials Research, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5B7, Canada
| | - Wing-Yiu Choy
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5C1, Canada; (C.J.W.); (M.C.)
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7
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Wang L, Wang Y, Yang Z, Xu S, Li H. Binding Selectivity of Inhibitors toward Bromodomains BAZ2A and BAZ2B Uncovered by Multiple Short Molecular Dynamics Simulations and MM-GBSA Calculations. ACS OMEGA 2021; 6:12036-12049. [PMID: 34056358 PMCID: PMC8154142 DOI: 10.1021/acsomega.1c00687] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/19/2021] [Indexed: 06/12/2023]
Abstract
Two Bromodomain-Containing proteins BAZ2A and BAZ2B are responsible for remodeling chromatin and regulating noncoding RNAs. As for our current studies, integration of multiple short molecular dynamics simulations (MSMDSs) with molecular mechanics generalized Born surface area (MM-GBSA) method is adopted for insights into binding selectivity of three small molecules D8Q, D9T and UO1 to BAZ2A against BAZ2B. The calculations of MM-GBSA unveil that selectivity of inhibitors toward BAZ2A and BAZ2B highly depends on the enthalpy changes and the details uncover that D8Q has better selectivity toward BAZ2A than BAZ2B, D9T more favorably bind to BAZ2B than BAZ2A, and UO1 does not show obvious selectivity toward these two proteins. The analysis of interaction network between residues and inhibitors indicates that seven residues are mainly responsible for the selectivity of D8Q, six residues for D9T and four residues provide significant contributions to associations of UO1 with two proteins. Moreover the analysis of interaction network not only reveals warm spots of inhibitor bindings to BAZ2A and BAZ2B but also unveils that common residue pairs, including (W1816, W1887), (P1817, P1888), (F1818, F1889), (V1822, V1893), (N1823, N1894),(L1826, L1897), (V1827, V1898), (F1872, F1943), (N1873, N1944) and (V1879, I1950) belonging to (BAZ2A, BAZ2B), induce mainly binding differences of inhibitors to BAZ2A and BAZ2B. Hence, insights from our current studies offer useful dynamics information relating with conformational alterations and structure-affinity relationship at atomistic levels for novel therapeutic strategies toward BAZ2A and BAZ2B.
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Affiliation(s)
- Lifei Wang
- School
of Science, Shandong Jiaotong University, 5001 Haitang Road, Changqing District, Jinan, Shandong Province 250357, China
| | - Yan Wang
- School
of Science, Shandong Jiaotong University, 5001 Haitang Road, Changqing District, Jinan, Shandong Province 250357, China
| | - Zhiyong Yang
- Department
of Physics, Jiangxi Agricultural University, 1101 Zhimin Road, Economic and Technological
Development Zone, Nanchang, Jiangxi Province 330045, China
| | - Shuobo Xu
- School
of Information Science and Electrical Engineering, Shandong Jiaotong University, 5001 Haitang Road, Changqing District, Jinan, Shandong Province 250357, China
| | - Hongyun Li
- School
of Science, Shandong Jiaotong University, 5001 Haitang Road, Changqing District, Jinan, Shandong Province 250357, China
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8
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Sahu SN, Satpathy SS, Mohanty C, Pattanayak SK. Computational study to evaluate the potency of phytochemicals in Boerhavia diffusa and the impact of point mutation on cyclin-dependent kinase 2-associated protein 1. J Biomol Struct Dyn 2021; 40:8587-8601. [PMID: 33876720 DOI: 10.1080/07391102.2021.1914169] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
A protein's function is closely related to its structural properties. Mutations can affect the functionality of a protein. Different cancer tissues have found disordered expression of the cyclin-dependent kinase 2-associated Protein 1 (CDK2AP1) gene. A protein molecule's conformational flexibility affects its interaction with phytochemicals and their biological partners at various levels. Boerhavia diffusa has been investigated most extensively for its medicinal activities like anticancer properties. It contains many bioactive compounds like Boeravinone A, Boeravinone B, Boeravinone C, Boeravinone D, Boeravinone E, Boeravinone F, Boeravinone G, Boeravinone H, Boeravinone I and Boeravinone J. We have studied to analyse the binding efficacy properties as well as essential dynamic behaviour, free energy landscape of both the native and mutant protein CDK2AP1 with bioactive compounds from Boerhavia diffusa plant extracts through computational approaches by homology modelling, docking and molecular dynamics simulation. From the molecular docking study, we found that. Boeravinone J have best binding affinity (-7.9 kcal/mol) towards the native protein of CDKAP1 compared to others phytochemicals. However, we found the binding energy for H23R and C105R (mutation point) -7.8 and -7.6 kcal/mol, respectively. A single minima energy point (from 100 ns molecular dynamics simulation study) was found in the H23R mutant with Boeravinone J complex suggested that minimum structural changes with less conformational mobility compared C105A mutant model.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Satya Narayan Sahu
- School of Applied Sciences, Kalinga Institute of Industrial Technology (KIIT) Deemed to be University, Bhubaneswar, India
| | - Sneha Shriparna Satpathy
- School of Applied Sciences, Kalinga Institute of Industrial Technology (KIIT) Deemed to be University, Bhubaneswar, India
| | - Chandana Mohanty
- School of Applied Sciences, Kalinga Institute of Industrial Technology (KIIT) Deemed to be University, Bhubaneswar, India
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9
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Fu C, Zhao L, Tan X, Li J, Wang X. Design and activity detection of BH3-mimetic peptide based on Bcl-X L binding potency. J Biomol Struct Dyn 2020; 38:4607-4616. [PMID: 31612794 DOI: 10.1080/07391102.2019.1680433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Chenggong Fu
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Longhe Zhao
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Xiangmin Tan
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Jiazhong Li
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Xin Wang
- School of Pharmacy, Lanzhou University, Lanzhou, China
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10
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Liu P, Zhang H, Wang Y, Chen X, Jin L, Xu L, Xiao M. Screening and characterization of an α-L-fucosidase from Bacteroides fragilis NCTC9343 for synthesis of fucosyl-N-acetylglucosamine disaccharides. Appl Microbiol Biotechnol 2020; 104:7827-7840. [PMID: 32715363 DOI: 10.1007/s00253-020-10759-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 06/18/2020] [Accepted: 06/29/2020] [Indexed: 11/30/2022]
Abstract
Fucosyl-N-acetylglucosamine disaccharides are present in many biologically important oligosaccharides, such as human milk oligosaccharides, Lewis carbohydrate antigens, and glycans on cell-surface glycoconjugate receptors, and thus have vast potential for infant formulas, prebiotics, and pharmaceutical applications. In this work, in order to screen biocatalysts for enzymatic synthesis of fucosyl-N-acetylglucosamine disaccharides, we performed sequence analysis of 12 putative and one known α-L-fucosidases of Bacteroides fragilis NCTC9343 and constructed a phylogenetic tree of the nine GH29 α-L-fucosidases. After that, five GH29A α-L-fucosidases were cloned, and four of them were successfully heterogeneous expressed and screened for transglycosylation activity, and a GH29A α-L-fucosidase (BF3242) that synthesized a mix of Fuc-α-1,3/1,6-GlcNAc disaccharides using pNPαFuc as donor and GlcNAc as acceptor was characterized. The effects of initial substrate concentration, pH, temperature, and reaction time on its transglycosylation activity were studied in detail. Under the optimum conditions of 0.05 U/mL enzyme, 20 mM pNPαFuc, and 500 mM GlcNAc in sodium buffer (pH 7.5) at 37 °C for 45 min, BF3242 efficiently synthesized Fuc-α-1,3/1,6-GlcNAc at a maximum yield of 79.0% with the ratio of 0.48 for 1,3/1,6. The molecular dynamics simulation analysis revealed that Loop-4 (His220-Ser245) in the putative 3D model of BF3242 displayed significant changes throughout the thermal simulations, might being responsible for the changes in the ratio of two regioisomeric products at different temperatures. This work provided not only a potential synthetic tool for enzymatic synthesis of fucosyl-N-acetylglucosamine disaccharides but also a possibility for the formation of regioisomeric products in glycosidase-catalyzed transglycosylation. KEY POINTS: • Sequence analysis of α-L-fucosidases of Bacteroides fragilis NCTC9343 • Obtainment of an α-L-fucosidase with high transglycosylation activity • Explanation why temperature affected the ratio of two regioisomeric products.
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Affiliation(s)
- Peng Liu
- State Key Lab of Microbial Technology, National Glycoengineering Research Center, Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Huaqin Zhang
- State Key Lab of Microbial Technology, National Glycoengineering Research Center, Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Yuying Wang
- State Key Lab of Microbial Technology, National Glycoengineering Research Center, Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Xiaodi Chen
- State Key Lab of Microbial Technology, National Glycoengineering Research Center, Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, 266237, People's Republic of China.,Department of Clinical Laboratory Medicine, Jinan Maternity and Child Care Hospital Affiliated to Shandong First Medical University, Jinan, 250001, People's Republic of China
| | - Lan Jin
- State Key Lab of Microbial Technology, National Glycoengineering Research Center, Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Li Xu
- State Key Lab of Microbial Technology, National Glycoengineering Research Center, Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, 266237, People's Republic of China.
| | - Min Xiao
- State Key Lab of Microbial Technology, National Glycoengineering Research Center, Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, 266237, People's Republic of China.
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Acosta-Tapia N, Galindo JF, Baldiris R. Insights into the Effect of Lowe Syndrome-Causing Mutation p.Asn591Lys of OCRL-1 through Protein-Protein Interaction Networks and Molecular Dynamics Simulations. J Chem Inf Model 2020; 60:1019-1027. [PMID: 31967472 DOI: 10.1021/acs.jcim.9b01077] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Inositol polyphosphate 5-phosphatase (OCRL-1) participates in the regulation of multiple cellular processes, through the conversion of phosphatidylinositol 4,5-phosphate to phosphatidylinositol 4-phosphate. Mutations in this protein are related to Lowe syndrome (LS) and Dent-2 disease. In this study, the impact of Lowe syndrome mutations on the interactions of OCRL-1 with other proteins was evaluated through bioinformatic and computational approaches. In the functional analysis of the interaction network of the proteins, we found that the terms of gene ontology (GO) of greater significance were related to the intracellular transport of proteins, the signal transduction mediated by small G proteins and vesicles associated with the Golgi apparatus. From the proteins present in the GO terms of greater significance Rab8a was selected because its interaction facilitates the intracellular distribution of OCRL-1. The mutation p.Asn591Lys, present in the interaction domain of OCRL-1 and Rab8a, was studied using molecular dynamics. The molecular dynamics analysis showed that the presence of this mutation causes changes in the positional fluctuations of the amino acids and affects the flexibility of the protein making the interaction with Rab8a weaker. Rab proteins establish some specific interactions, which are important for the intracellular localization of OCRL-1; therefore, our findings suggest that the phenotype observed in patients with LS, in this case, is due to the destabilizing effect of p.Asn591Lys affecting the localization of OCRL-1 and indirectly its 5-phosphatase activity in the Golgi apparatus, endosomes, and cilia.
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Affiliation(s)
- Natali Acosta-Tapia
- Programa de Biologı́a, Facultad de Ciencias Exactas y Naturales , Universidad de Cartagena , Cartagena de Indias , Colombia.,Grupo de Investigación CIPTEC, Facultad de Ingenierı́a , Fundación Universitaria Tecnológico Comfenalco , Cartagena de Indias 130015 , Colombia
| | - Johan Fabian Galindo
- Departamento de Quı́mica , Universidad Nacional de Colombia , Bogotá 111321 , Colombia
| | - Rosa Baldiris
- Programa de Biologı́a, Facultad de Ciencias Exactas y Naturales , Universidad de Cartagena , Cartagena de Indias , Colombia.,Grupo de Investigación CIPTEC, Facultad de Ingenierı́a , Fundación Universitaria Tecnológico Comfenalco , Cartagena de Indias 130015 , Colombia
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13
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Mariadasse R, Choubey SK, Jeyakanthan J. Insights into Exogenous Tryptophan-Mediated Allosteric Communication and Helical Transition of TRP Protein for Transcription Regulation. J Chem Inf Model 2019; 60:175-191. [DOI: 10.1021/acs.jcim.9b00755] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Richard Mariadasse
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, 630 004 Tamil Nadu, India
| | - Sanjay Kumar Choubey
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, 630 004 Tamil Nadu, India
| | - Jeyaraman Jeyakanthan
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, 630 004 Tamil Nadu, India
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14
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Ruete MC, Zarelli VEP, Masone D, de Paola M, Bustos DM, Tomes CN. A connection between reversible tyrosine phosphorylation and SNARE complex disassembly activity of N-ethylmaleimide-sensitive factor unveiled by the phosphomimetic mutant N-ethylmaleimide-sensitive factor-Y83E. ACTA ACUST UNITED AC 2019; 25:344-358. [DOI: 10.1093/molehr/gaz031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 05/16/2019] [Accepted: 06/03/2019] [Indexed: 12/26/2022]
Abstract
Abstract
N-ethylmaleimide-sensitive factor (NSF) disassembles fusion-incompetent cis soluble-NSF attachment protein receptor (SNARE) complexes making monomeric SNAREs available for subsequent trans pairing and fusion. In most cells the activity of NSF is constitutive, but in Jurkat cells and sperm it is repressed by tyrosine phosphorylation; the phosphomimetic mutant NSF–Y83E inhibits secretion in the former. The questions addressed here are if and how the NSF mutant influences the configuration of the SNARE complex. Our model is human sperm, where the initiation of exocytosis (acrosome reaction (AR)) de-represses the activity of NSF through protein tyrosine phosphatase 1B (PTP1B)-mediated dephosphorylation. We developed a fluorescence microscopy-based method to show that capacitation increased, and challenging with an AR inducer decreased, the number of cells with tyrosine-phosphorylated PTP1B substrates in the acrosomal domain. Results from bioinformatic and biochemical approaches using purified recombinant proteins revealed that NSF–Y83E bound PTP1B and thereupon inhibited its catalytic activity. Mutant NSF introduced into streptolysin O-permeabilized sperm impaired cis SNARE complex disassembly, blocking the AR; subsequent addition of PTP1B rescued exocytosis. We propose that NSF–Y83E prevents endogenous PTP1B from dephosphorylating sperm NSF, thus maintaining NSF’s activity in a repressed mode and the SNARE complex unable to dissociate. The contribution of this paper to the sperm biology field is the detection of PTP1B substrates, one of them likely being NSF, whose tyrosine phosphorylation status varies during capacitation and the AR. The contribution of this paper to the membrane traffic field is to have generated direct evidence that explains the dominant-negative role of the phosphomimetic mutant NSF–Y83E.
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Affiliation(s)
- María Celeste Ruete
- Instituto de Histología y Embriología de Mendoza Dr Mario H. Burgos–CONICET, Universidad Nacional de Cuyo, Mendoza, Argentina
| | - Valeria Eugenia Paola Zarelli
- Instituto de Histología y Embriología de Mendoza Dr Mario H. Burgos–CONICET, Universidad Nacional de Cuyo, Mendoza, Argentina
- Facultad de Ciencias Médicas, Universidad Nacional de Cuyo, Mendoza, Argentina
| | - Diego Masone
- Instituto de Histología y Embriología de Mendoza Dr Mario H. Burgos–CONICET, Universidad Nacional de Cuyo, Mendoza, Argentina
- Facultad de Ingeniería, Universidad Nacional de Cuyo, Mendoza, Argentina
| | - Matilde de Paola
- Instituto de Histología y Embriología de Mendoza Dr Mario H. Burgos–CONICET, Universidad Nacional de Cuyo, Mendoza, Argentina
- Facultad de Ciencias Médicas, Universidad Nacional de Cuyo, Mendoza, Argentina
- Instituto de Medicina y Biología Experimental de Cuyo–Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Cuyo, Mendoza, Argentina
| | - Diego Martín Bustos
- Instituto de Histología y Embriología de Mendoza Dr Mario H. Burgos–CONICET, Universidad Nacional de Cuyo, Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Mendoza, Argentina
| | - Claudia Nora Tomes
- Instituto de Histología y Embriología de Mendoza Dr Mario H. Burgos–CONICET, Universidad Nacional de Cuyo, Mendoza, Argentina
- Facultad de Ciencias Médicas, Universidad Nacional de Cuyo, Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Mendoza, Argentina
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15
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Zhang H, Song T, Yang Y, Fu C, Li J. Exploring the Interaction Mechanism Between Cyclopeptide DC3 and Androgen Receptor Using Molecular Dynamics Simulations and Free Energy Calculations. Front Chem 2018; 6:119. [PMID: 29755968 PMCID: PMC5932393 DOI: 10.3389/fchem.2018.00119] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 03/30/2018] [Indexed: 01/10/2023] Open
Abstract
Androgen receptor (AR) is a key target in the discovery of anti-PCa (Prostate Cancer) drugs. Recently, a novel cyclopeptide Diffusa Cyclotide-3 (DC3), isolated from Hedyotisdiffusa, has been experimentally demonstrated to inhibit the survival and growth of LNCap cells, which typically express T877A-mutated AR, the most frequently detected point mutation of AR in castration-resistant prostate cancer (CRPC). But the interaction mechanism between DC3 and AR is not clear. Here in this study we aim to explore the possible binding mode of DC3 to T877A-mutated AR from molecular perspective. Firstly, homology modeling was employed to construct the three-dimensional structure of the cyclopeptide DC3 using 2kux.1.A as the template. Then molecular docking, molecular dynamics (MD) simulations, and molecular mechanics/generalized Born surface area (MM-GBSA) methods were performed to determine the bind site and explore the detailed interaction mechanism of DC3-AR complex. The obtained results suggested that the site formed by H11, loop888-893, and H12 (site 2) was the most possible position of DC3 binding to AR. Besides, hydrogen bonds, hydrophobic, and electrostatic interactions play dominant roles in the recognition and combination of DC3-AR complex. The essential residues dominant in each interaction were specifically revealed. This work facilitates our understanding of the interaction mechanism of DC3 binding to AR at the molecular level and contributes to the rational cyclopeptide drug design for prostate cancer.
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Affiliation(s)
- Huimin Zhang
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Tianqing Song
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Yizhao Yang
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, China
| | - Chenggong Fu
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Jiazhong Li
- School of Pharmacy, Lanzhou University, Lanzhou, China
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16
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Structural Basis for the Influence of A1, 5A, and W51W57 Mutations on the Conductivity of the Geobacter sulfurreducens Pili. CRYSTALS 2017. [DOI: 10.3390/cryst8010010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The metallic-like conductivity of the Geobacter sulfurreducens pilus and higher conductivity of its mutants reflected that biological synthesis can be utilized to improve the properties of electrically conductive pili. However, the structural basis for diverse conductivities of nanowires remains uncertain. Here, the impacts of point mutations on the flexibility and stability of pilins were investigated based on molecular dynamics simulations. Structures of the G. sulfurreducens pilus and its mutants were constructed by Rosetta. Details of the structure (i.e., electrostatic properties, helical parameters, residue interaction network, distances between amino acids, and salt bridges) were analyzed by PDB2PQR, Rosetta, RING, PyMOL, and VMD, respectively. Changes in stability, flexibility, residue interaction, and electrostatic properties of subunits directly caused wild-type pilin and its mutants assemble different structures of G. sulfurreducens pili. By comparing the structures of pili with different conductivities, the mechanism by which the G. sulfurreducens pilus transfers electron along pili was attributed, at least in part, to the density of aromatic rings, the distances between neighboring aromatic rings, and the local electrostatic environment around aromatic contacts. These results provide new insight into the potential for the biological synthesis of highly electrically conductive, nontoxic nanowires.
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17
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Yan F, Liu X, Zhang S, Su J, Zhang Q, Chen J. Computational revelation of binding mechanisms of inhibitors to endocellular protein tyrosine phosphatase 1B using molecular dynamics simulations. J Biomol Struct Dyn 2017; 36:3636-3650. [DOI: 10.1080/07391102.2017.1394221] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Fangfang Yan
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China
| | - Xinguo Liu
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China
| | - Shaolong Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China
| | - Jing Su
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China
| | - Qinggang Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China
| | - Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan, 250357, China
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18
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Wu X, Tian Z, Jiang X, Zhang Q, Wang L. Enhancement in catalytic activity of Aspergillus niger XynB by selective site-directed mutagenesis of active site amino acids. Appl Microbiol Biotechnol 2017; 102:249-260. [DOI: 10.1007/s00253-017-8607-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 10/10/2017] [Accepted: 10/12/2017] [Indexed: 01/25/2023]
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19
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Kayık G, Tüzün NŞ, Durdagi S. Structural investigation of vesnarinone at the pore domains of open and open-inactivated states of hERG1 K + channel. J Mol Graph Model 2017; 77:399-412. [DOI: 10.1016/j.jmgm.2017.08.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 08/17/2017] [Accepted: 08/18/2017] [Indexed: 12/22/2022]
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20
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Substrate binding interferes with active site conformational dynamics in endoglucanase Cel5A from Thermobifida fusca. Biochem Biophys Res Commun 2017; 491:236-240. [DOI: 10.1016/j.bbrc.2017.07.086] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 07/14/2017] [Indexed: 11/16/2022]
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21
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Nguyen H, Do N, Phan T, Pham T. Steered Molecular Dynamics for Investigating the Interactions Between Insulin Receptor Tyrosine Kinase (IRK) and Variants of Protein Tyrosine Phosphatase 1B (PTP1B). Appl Biochem Biotechnol 2017; 184:401-413. [DOI: 10.1007/s12010-017-2549-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 06/25/2017] [Indexed: 11/30/2022]
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22
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Way MJ, Ali MA, McQuillin A, Morgan MY. Genetic variants in ALDH1B1 and alcohol dependence risk in a British and Irish population: A bioinformatic and genetic study. PLoS One 2017; 12:e0177009. [PMID: 28594837 PMCID: PMC5464525 DOI: 10.1371/journal.pone.0177009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 04/20/2017] [Indexed: 12/30/2022] Open
Abstract
Alcohol is metabolized in the liver via the enzymes alcohol dehydrogenase (ADH) and aldehyde dehydrogenase (ALDH). Polymorphisms in the genes encoding these enzymes, which are common in East Asian populations, can alter enzyme kinetics and hence the risk of alcohol dependence and its sequelae. One of the most important genetic variants, in this regards, is the single nucleotide polymorphism (SNP) rs671 in ALDH2, the gene encoding the primary acetaldehyde metabolizing enzyme ALDH2. However, the protective allele of rs671 is absent in most Europeans although ALDH1B1, which shares significant sequence homology with ALDH2, contains several, potentially functional, missense SNPs that do occur in European populations. The aims of this study were: (i) to use bioinformatic techniques to characterize the possible effects of selected variants in ALDH1B1 on protein structure and function; and, (ii) to genotype three missense and one stop-gain, protein-altering, non-synonymous SNPs in 1478 alcohol dependent cases and 1254 controls of matched British and Irish ancestry. No significant allelic associations were observed between the three missense SNPs and alcohol dependence risk. The minor allele frequency of rs142427338 (Gln378Ter) was higher in alcohol dependent cases than in controls (allelic P = 0.19, OR = 2.98, [0.62–14.37]) but as this SNP is very rare the study was likely underpowered to detect an association with alcohol dependence risk. This potential association will needs to be further evaluated in other large, independent European populations.
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Affiliation(s)
- Michael J. Way
- Molecular Psychiatry Laboratory, Division of Psychiatry, University College London, London, United Kingdom
- UCL Institute for Liver & Digestive Health, Department of Medicine, Royal Free Campus, University College London, London, United Kingdom
| | - M. Adam Ali
- Molecular Psychiatry Laboratory, Division of Psychiatry, University College London, London, United Kingdom
- UCL Institute for Liver & Digestive Health, Department of Medicine, Royal Free Campus, University College London, London, United Kingdom
| | - Andrew McQuillin
- Molecular Psychiatry Laboratory, Division of Psychiatry, University College London, London, United Kingdom
| | - Marsha Y. Morgan
- UCL Institute for Liver & Digestive Health, Department of Medicine, Royal Free Campus, University College London, London, United Kingdom
- * E-mail:
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23
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Aeksiri N, Jantafong T. Structural insights into type I and type II of nsp4 porcine reproductive and respiratory syndrome virus (nsp4 PRRSV) by molecular dynamics simulations. J Mol Graph Model 2017; 74:125-134. [PMID: 28411461 PMCID: PMC7110526 DOI: 10.1016/j.jmgm.2017.03.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 03/16/2017] [Accepted: 03/17/2017] [Indexed: 01/28/2023]
Abstract
Porcine reproductive and respiratory virus (PRRSV) causes major economic concerns for the swine industry worldwide. We have performed molecular dynamics simulations (MD) and principle component analysis (PCA) to investigate the role of the catalytic triad and conformational dynamics of type I and type II of nsp4 PRRSV. The results showed that the RMSF of residues 136-142 near the active site of all models was highly flexible. Moreover, we identified the effect of single structural mutations of the catalytic triad. The percentage of residue with a 0.1nm RMSF value and PCA results revealed that the mutations affected domain I and II suggesting the wild types were more stable than the mutants. At the catalytic triad, the distances between H39 and S118 were very flexible while the distances between H39 and D64 were very stable. H39, D64 and S118 showed high occupancy percentage of the hydrogen bond interaction with many residues that are conserved in PRRSVAS, PRRSVES, LDVC, LDVP and EAV. Moreover, S118 of wild-type protein formed H-bonds with T134 and G135 but these interactions were lost in PRRSVAV (S118A) and PRRSVES (S117A) indicating that the substitution of important H-bond interaction in PRRSVAS (S118A) and PRRSVES (S117A) affected the flexibility around the catalytic triad, conformation and proteolytic activity. Overall, our study may provide the structural basic of the catalytic triad and be useful for testing the protein activity in future experiments.
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Affiliation(s)
- Niran Aeksiri
- Center for Agriculture Biotechnology, Faculty of Agriculture, Natural Resources, and Environment, Naresuan University, Phitsanulok 65000, Thailand; Department of Agricultural Sciences, Faculty of Agriculture, Natural Resources, and Environment, Naresuan University, Phitsanulok 65000, Thailand.
| | - Tippawan Jantafong
- Department of Virology and Immunology, Faculty of Veterinary Medicine, Mahanakorn University of Technology, Thailand
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24
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Jiang X, Li W, Chen G, Wang L. Dynamic Perturbation of the Active Site Determines Reversible Thermal Inactivation in Glycoside Hydrolase Family 12. J Chem Inf Model 2017; 57:288-297. [DOI: 10.1021/acs.jcim.6b00692] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xukai Jiang
- State Key Laboratory
of Microbial
Technology, Shandong University, Jinan 250100, China
| | - Wen Li
- State Key Laboratory
of Microbial
Technology, Shandong University, Jinan 250100, China
| | - Guanjun Chen
- State Key Laboratory
of Microbial
Technology, Shandong University, Jinan 250100, China
| | - Lushan Wang
- State Key Laboratory
of Microbial
Technology, Shandong University, Jinan 250100, China
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25
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Porto WF, Nolasco DO, Pires ÁS, Pereira RW, Franco OL, Alencar SA. Prediction of the impact of coding missense and nonsense single nucleotide polymorphisms on HD5 and HBD1 antibacterial activity against Escherichia coli. Biopolymers 2017; 106:633-44. [PMID: 27160989 DOI: 10.1002/bip.22866] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 03/14/2016] [Accepted: 04/26/2016] [Indexed: 01/01/2023]
Abstract
Defensins confer host defense against microorganisms and are important for human health. Single nucleotide polymorphisms (SNPs) in defensin gene-coding regions could lead to less active variants. Using SNP data available at the dbSNP database and frequency information from the 1000 Genomes Project, two DEFA5 (L26I and R13H) and eight DEFB1 (C35S, K31T, K33R, R29G, V06I, C12Y, Y28* and C05*) missense and nonsense SNPs that are located within mature regions of the coded defensins were retrieved. Such SNPs are rare and population restricted. In order to assess their antibacterial activity against Escherichia coli, two linear regression models were used from a previous work, which models the antibacterial activity as a function of solvation potential energy, using molecular dynamics data. Regarding only the antibacterial predictions, for HD5, no biological differences between wild-type and its variants were observed; while for HBD1, the results suggest that the R29G, K31T, Y28* and C05* variants could be less active than the wild-type one. The data here reported could lead to a substantial improvement in knowledge about the impact of missense SNPs in human defensins and their world distribution. © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 633-644, 2016.
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Affiliation(s)
- William F Porto
- Programa De Pós-Graduação Em Ciências Genômicas E Biotecnologia, Universidade Católica De Brasília, Brasília, DF, Brazil.,Centro De Análises Proteômicas E Bioquímicas, Pós-Graduação Em Ciências Genômicas E Biotecnologia, Universidade Católica De Brasília, Brasília, DF, Brazil
| | - Diego O Nolasco
- Programa De Pós-Graduação Em Ciências Genômicas E Biotecnologia, Universidade Católica De Brasília, Brasília, DF, Brazil.,Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA
| | - Állan S Pires
- Programa De Pós-Graduação Em Ciências Genômicas E Biotecnologia, Universidade Católica De Brasília, Brasília, DF, Brazil.,Centro De Análises Proteômicas E Bioquímicas, Pós-Graduação Em Ciências Genômicas E Biotecnologia, Universidade Católica De Brasília, Brasília, DF, Brazil
| | - Rinaldo W Pereira
- Programa De Pós-Graduação Em Ciências Genômicas E Biotecnologia, Universidade Católica De Brasília, Brasília, DF, Brazil
| | - Octávio L Franco
- Programa De Pós-Graduação Em Ciências Genômicas E Biotecnologia, Universidade Católica De Brasília, Brasília, DF, Brazil. .,Centro De Análises Proteômicas E Bioquímicas, Pós-Graduação Em Ciências Genômicas E Biotecnologia, Universidade Católica De Brasília, Brasília, DF, Brazil. .,S-Inova Biotech, Pos-Graduação Em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil.
| | - Sérgio A Alencar
- Programa De Pós-Graduação Em Ciências Genômicas E Biotecnologia, Universidade Católica De Brasília, Brasília, DF, Brazil
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26
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Zhao D, Zhou J. Electrostatics-mediated α-chymotrypsin inhibition by functionalized single-walled carbon nanotubes. Phys Chem Chem Phys 2017; 19:986-995. [DOI: 10.1039/c6cp04962a] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Electrostatics-mediated α-chymotrypsin inhibition by functionalized single-walled carbon nanotubes.
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Affiliation(s)
- Daohui Zhao
- School of Chemistry and Chemical Engineering
- Guangdong Provincial Key Lab for Green Chemical Product Technology
- South China University of Technology
- Guangzhou
- P. R. China
| | - Jian Zhou
- School of Chemistry and Chemical Engineering
- Guangdong Provincial Key Lab for Green Chemical Product Technology
- South China University of Technology
- Guangzhou
- P. R. China
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27
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Marimuthu P, Singaravelu K, Namasivayam V. Probing the binding mechanism of mercaptoguanine derivatives as inhibitors of HPPK by docking and molecular dynamics simulations. J Biomol Struct Dyn 2016; 35:3507-3521. [PMID: 27844507 DOI: 10.1080/07391102.2016.1260496] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) is a promising antimicrobial target involved in the folate biosynthesis pathway. Although, the results from crystallographic studies of HPPK have attracted a great interest in the design of novel HPPK inhibitors, the mechanism of action of HPPK due to inhibitor binding remains questionable. Recently, mercaptoguanine derivatives were reported to inhibit the pyrophosphoryl transfer mechanism of Staphylococcus aureus HPPK (SaHPPK). The present study is an attempt to understand the SaHPPK-inhibitors binding mechanism and to highlight the key residues that possibly involve in the complex formation. To decipher these questions, we used the state-of-the-art advanced insilico approach such as molecular docking, molecular dynamics (MD), molecular mechanics-generalized Born surface area approach. Domain cross correlation and principle component analysis were applied to the snapshots obtained from MD revealed that the compounds with high binding affinity stabilize the conformational dynamics of SaHPPK. The binding free energy estimation showed that the van der Waals and electrostatic interactions played a vital role for the binding mechanism. Additionally, the predicted binding free energy was in good agreement with the experimental values (R2 = .78). Moreover, the free energy decomposition on per-residue confirms the key residues that significantly contribute to the complex formation. These results are expected to be useful for rational design of novel SaHPPK inhibitors.
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Affiliation(s)
- Parthiban Marimuthu
- a Structural Bioinformatics Laboratory (SBL), Faculty of Science and Engineering , Åbo Akademi University , Turku FI-20520 , Finland
| | - Kalaimathy Singaravelu
- b Department of Information Technology, Turku Centre for Biotechnology , University of Turku , Turku FI-20520 , Finland
| | - Vigneshwaran Namasivayam
- c PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry II , University of Bonn , An der Immenburg 4, Bonn D-53121 , Germany
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28
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Effects of interface mutations on the dimerization of alanine glyoxylate aminotransferase and implications in the mistargeting of the pathogenic variants F152I and I244T. Biochimie 2016; 131:137-148. [PMID: 27720751 DOI: 10.1016/j.biochi.2016.10.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 10/02/2016] [Accepted: 10/02/2016] [Indexed: 11/21/2022]
Abstract
In this work the dimerization process of the minor allelic form of human alanine glyoxylate aminotransferase, a pyridoxal 5'-phosphate enzyme, was investigated. Bioinformatic analyses followed by site-directed mutagenesis, size exclusion chromatography and catalytic activity experiments allowed us to identify Arg118, Phe238 and Phe240 as interfacial residues not essential for transaminase activity but important for dimer-monomer dissociation. The apo and the holo forms of the triple mutant R118A-Mi/F238S-Mi/F240S-Mi display a dimer-monomer equilibrium dissociation constant value at least ~260- and 31-fold larger, respectively, than the corresponding ones of AGT-Mi. In the presence of PLP, the apomonomer of the triple mutant undergoes a biphasic process: the fast phase represents the formation of an inactive PLP-bound monomer, while the slow phase depicts the monomer-monomer association that parallels the regain of transaminase activity. The latter events occur with a rate constant of ~0.02 μM-1min-1. In the absence of PLP, the apomonomer is also able to dimerize but with a rate constant value ~2700-fold lower. Thereafter, the possible interference with the dimerization process of AGT-Mi exerted by the mutated residues in the I244T-Mi and F152I-Mi variants associated with Primary Hyperoxaluria type 1 was investigated by molecular dynamics simulations. On the basis of the present and previous studies, a model for the dimerization process of AGT-Mi, I244T-Mi and F152I-Mi, which outlines the structural defects responsible for the complete or partial mistargeting of the pathogenic variants, was proposed and discussed.
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29
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Rajendran V, Gopalakrishnan C, Purohit R. Impact of point mutation P29S in RAC1 on tumorigenesis. Tumour Biol 2016; 37:15293-15304. [DOI: 10.1007/s13277-016-5329-y] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 09/06/2016] [Indexed: 01/07/2023] Open
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30
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Thirumal Kumar D, George Priya Doss C, Sneha P, Tayubi IA, Siva R, Chakraborty C, Magesh R. Influence of V54M mutation in giant muscle protein titin: a computational screening and molecular dynamics approach. J Biomol Struct Dyn 2016; 35:917-928. [PMID: 27125723 DOI: 10.1080/07391102.2016.1166456] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Recent genetic studies have revealed the impact of mutations in associated genes for cardiac sarcomere components leading to dilated cardiomyopathy (DCM). The cardiac sarcomere is composed of thick and thin filaments and a giant muscle protein known as titin or connectin. Titin interacts with T-cap/telethonin in the Z-line region and plays a vital role in regulating sarcomere assembly. Initially, we screened all the variants associated with giant protein titin and analyzed their impact with the aid of pathogenicity and stability prediction methods. V54M mutation found in the hydrophobic core region of the protein associated with abnormal clinical phenotype leads to DCM was selected for further analysis. To address this issue, we mapped the deleterious mutant V54M, modeled the mutant protein complex, and deciphered the impact of mutation on binding with its partner telethonin in the titin crystal structure of PDB ID: 1YA5 with the aid of docking analysis. Furthermore, two run molecular dynamics simulation was initiated to understand the mechanistic action of V54M mutation in altering the protein structure, dynamics, and stability. According to the results obtained from the repeated 50 ns trajectory files, the overall effect of V54M mutation was destabilizing and transition of bend to coil in the secondary structure was observed. Furthermore, MMPBSA elucidated that V54M found in the Z-line region of titin decreases the binding affinity of titin to Z-line proteins T-cap/telethonin thereby hindering the protein-protein interaction.
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Affiliation(s)
- D Thirumal Kumar
- a School of Biosciences and Technology , VIT University , Vellore , Tamil Nadu 632014 , India
| | - C George Priya Doss
- a School of Biosciences and Technology , VIT University , Vellore , Tamil Nadu 632014 , India
| | - P Sneha
- a School of Biosciences and Technology , VIT University , Vellore , Tamil Nadu 632014 , India
| | - Iftikhar Aslam Tayubi
- a School of Biosciences and Technology , VIT University , Vellore , Tamil Nadu 632014 , India.,b Faculty of Computing and Information Technology , King Abdulaziz University , Rabigh 21911 , Saudi Arabia
| | - R Siva
- a School of Biosciences and Technology , VIT University , Vellore , Tamil Nadu 632014 , India
| | - Chiranjib Chakraborty
- c Department of Bio-informatics , School of Computer and Information Sciences, Galgotias University , Greater Noida , Uttar Pradesh 201306 , India
| | - R Magesh
- d Faculty of Biomedical Sciences, Technology & Research, Department of Biotechnology , Sri Ramachandra University , Chennai , Tamil Nadu 600116 , India
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Porto WF, Nolasco DO, Pires ÁS, Fernandes GR, Franco OL, Alencar SA. HD5 and HBD1 variants’ solvation potential energy correlates with their antibacterial activity against Escherichia coli. Biopolymers 2016; 106:43-50. [DOI: 10.1002/bip.22763] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2015] [Revised: 10/22/2015] [Accepted: 11/02/2015] [Indexed: 11/06/2022]
Affiliation(s)
- William F. Porto
- Programa De Pós-Graduação Em Ciências Genômicas E Biotecnologia; Universidade Católica De Brasília; Brasília- DF Brazil
- Centro De Análises Proteômicas E Bioquímicas, Pós-Graduação Em Ciências Genômicas E Biotecnologia; Universidade Católica De Brasília; Brasília- DF Brazil
| | - Diego O. Nolasco
- Programa De Pós-Graduação Em Ciências Genômicas E Biotecnologia; Universidade Católica De Brasília; Brasília- DF Brazil
- Curso De Física; Universidade Católica De Brasília; Brasília DF Brazil
| | - Állan S. Pires
- Programa De Pós-Graduação Em Ciências Genômicas E Biotecnologia; Universidade Católica De Brasília; Brasília- DF Brazil
- Centro De Análises Proteômicas E Bioquímicas, Pós-Graduação Em Ciências Genômicas E Biotecnologia; Universidade Católica De Brasília; Brasília- DF Brazil
| | - Gabriel R. Fernandes
- Programa De Pós-Graduação Em Ciências Genômicas E Biotecnologia; Universidade Católica De Brasília; Brasília- DF Brazil
| | - Octávio L. Franco
- Programa De Pós-Graduação Em Ciências Genômicas E Biotecnologia; Universidade Católica De Brasília; Brasília- DF Brazil
- Centro De Análises Proteômicas E Bioquímicas, Pós-Graduação Em Ciências Genômicas E Biotecnologia; Universidade Católica De Brasília; Brasília- DF Brazil
- S-Inova Biotech; Pos Graduação em Biotecnologia; Universidade Catolica Dom Bosco; Campo Grande Campo Grande Brazil
| | - Sérgio A. Alencar
- Programa De Pós-Graduação Em Ciências Genômicas E Biotecnologia; Universidade Católica De Brasília; Brasília- DF Brazil
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Jiang X, Chen G, Wang L. Structural and dynamic evolution of the amphipathic N-terminus diversifies enzyme thermostability in the glycoside hydrolase family 12. Phys Chem Chem Phys 2016; 18:21340-50. [DOI: 10.1039/c6cp02998a] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The N-terminus diversifies enzyme thermostability in the GH12 family, which was investigated by MD simulations, and provides potential applications in protein engineering.
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Affiliation(s)
- Xukai Jiang
- State Key Laboratory of Microbial Technology
- Shandong University
- Jinan 250100
- China
| | - Guanjun Chen
- State Key Laboratory of Microbial Technology
- Shandong University
- Jinan 250100
- China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology
- Shandong University
- Jinan 250100
- China
- State Key Laboratory of Biochemical Engineering
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Chen J, Wang J, Zhang Q, Chen K, Zhu W. Probing Origin of Binding Difference of inhibitors to MDM2 and MDMX by Polarizable Molecular Dynamics Simulation and QM/MM-GBSA Calculation. Sci Rep 2015; 5:17421. [PMID: 26616018 PMCID: PMC4663504 DOI: 10.1038/srep17421] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 10/29/2015] [Indexed: 12/13/2022] Open
Abstract
Binding abilities of current inhibitors to MDMX are weaker than to MDM2. Polarizable molecular dynamics simulations (MD) followed by Quantum mechanics/molecular mechanics generalized Born surface area (QM//MM-GBSA) calculations were performed to investigate the binding difference of inhibitors to MDM2 and MDMX. The predicted binding free energies not only agree well with the experimental results, but also show that the decrease in van der Walls interactions of inhibitors with MDMX relative to MDM2 is a main factor of weaker bindings of inhibitors to MDMX. The analyses of dihedral angles based on MD trajectories suggest that the closed conformation formed by the residues M53 and Y99 in MDMX leads to a potential steric clash with inhibitors and prevents inhibitors from arriving in the deep of MDMX binding cleft, which reduces the van der Waals contacts of inhibitors with M53, V92, P95 and L98. The calculated results using the residue-based free energy decomposition method further prove that the interaction strength of inhibitors with M53, V92, P95 and L98 from MDMX are obviously reduced compared to MDM2. We expect that this study can provide significant theoretical guidance for designs of potent dual inhibitors to block the p53-MDM2/MDMX interactions.
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Affiliation(s)
- Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan, 250014, China
| | - Jinan Wang
- Discovery and Design Center, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
| | - Qinggang Zhang
- College of Physics and Electronics, Shandong Normal University, Jinan, 250014, China
| | - Kaixian Chen
- Discovery and Design Center, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
| | - Weiliang Zhu
- Discovery and Design Center, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
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Cheng W, Liang Z, Wang W, Yi C, Li H, Zhang S, Zhang Q. Insight into binding modes of p53 and inhibitors to MDM2 based on molecular dynamic simulations and principal component analysis. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1087598] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Porto WF, Franco OL, Alencar SA. Computational analyses and prediction of guanylin deleterious SNPs. Peptides 2015; 69:92-102. [PMID: 25899674 DOI: 10.1016/j.peptides.2015.04.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 04/10/2015] [Accepted: 04/12/2015] [Indexed: 01/01/2023]
Abstract
Human guanylin, coded by the GUCA2A gene, is a member of a peptide family that activates intestinal membrane guanylate cyclase, regulating electrolyte and water transport in intestinal and renal epithelia. Deregulation of guanylin peptide activity has been associated with colon adenocarcinoma, adenoma and intestinal polyps. Besides, it is known that mutations on guanylin receptors could be involved in meconium ileus. However, there are no previous works regarding the alterations driven by single nucleotide polymorphisms in guanylin peptides. A comprehensive in silico analysis of missense SNPs present in the GUCA2A gene was performed taking into account 16 prediction tools in order to select the deleterious variations for further evaluation by molecular dynamics simulations (50 ns). Molecular dynamics data suggest that the three out of five variants (Cys104Arg, Cys112Ser and Cys115Tyr) have undergone structural modifications in terms of flexibility, volume and/or solvation. In addition, two nonsense SNPs were identified, both preventing the formation of disulfide bonds and resulting in the synthesis of truncated proteins. In summary the structural analysis of missense SNPs is important to decrease the number of potential mutations to be in vitro evaluated for associating them with some genetic diseases. In addition, data reported here could lead to a better understanding of structural and functional aspects of guanylin peptides.
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Affiliation(s)
- William F Porto
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil; Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil
| | - Octávio L Franco
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil; Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil; C S-Inova, Pos-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil.
| | - Sérgio A Alencar
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil.
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Chen J, Liang Z, Wang W, Yi C, Zhang S, Zhang Q. Revealing origin of decrease in potency of darunavir and amprenavir against HIV-2 relative to HIV-1 protease by molecular dynamics simulations. Sci Rep 2014; 4:6872. [PMID: 25362963 PMCID: PMC4217091 DOI: 10.1038/srep06872] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 10/13/2014] [Indexed: 12/30/2022] Open
Abstract
Clinical inhibitors Darunavir (DRV) and Amprenavir (APV) are less effective on HIV-2 protease (PR2) than on HIV-1 protease (PR1). To identify molecular basis associated with the lower inhibition, molecular dynamics (MD) simulations and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) calculations were performed to investigate the effectiveness of the PR1 inhibitors DRV and APV against PR1/PR2. The rank of predicted binding free energies agrees with the experimental determined one. Moreover, our results show that two inhibitors bind less strongly to PR2 than to PR1, again in agreement with the experimental findings. The decrease in binding free energies for PR2 relative to PR1 is found to arise from the reduction of the van der Waals interactions induced by the structural adjustment of the triple mutant V32I, I47V and V82I. This result is further supported by the difference between the van der Waals interactions of inhibitors with each residue in PR2 and in PR1. The results from the principle component analysis suggest that inhibitor binding tends to make the flaps of PR2 close and the one of PR1 open. We expect that this study can theoretically provide significant guidance and dynamics information for the design of potent dual inhibitors targeting PR1/PR2.
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Affiliation(s)
- Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan 250357, China
| | - Zhiqiang Liang
- School of Science, Shandong Jiaotong University, Jinan 250357, China
| | - Wei Wang
- School of Science, Shandong Jiaotong University, Jinan 250357, China
| | - Changhong Yi
- School of Science, Shandong Jiaotong University, Jinan 250357, China
| | - Shaolong Zhang
- College of Physics and Electronics, Shandong Normal University, Jinan, 250014, China
| | - Qinggang Zhang
- College of Physics and Electronics, Shandong Normal University, Jinan, 250014, China
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