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Li XN, Gao Y, Li Y, Yin JX, Yi CW, Yuan HY, Huang JJ, Wang LQ, Chen J, Liang Y. Arg177 and Asp159 from dog prion protein slow liquid-liquid phase separation and inhibit amyloid formation of human prion protein. J Biol Chem 2023; 299:105329. [PMID: 37805139 PMCID: PMC10641668 DOI: 10.1016/j.jbc.2023.105329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 08/23/2023] [Accepted: 09/05/2023] [Indexed: 10/09/2023] Open
Abstract
Prion diseases are a group of transmissible neurodegenerative diseases primarily caused by the conformational conversion of prion protein (PrP) from α-helix-dominant cellular prion protein (PrPC) to β-sheet-rich pathological aggregated form of PrPSc in many mammalian species. Dogs exhibit resistance to prion diseases, but the mechanism behind the phenomenon remains poorly understood. Compared with human PrP and mouse PrP, dog PrP has two unique amino acid residues, Arg177 and Asp159. Because PrPC contains a low-complexity and intrinsically disordered region in its N-terminal domain, it undergoes liquid-liquid phase separation (LLPS) in vitro and forms protein condensates. However, little is known about whether these two unique residues modulate the formation of PrPC condensates. Here, using confocal microscopy, fluorescence recovery after photobleaching assays, thioflavin T binding assays, and transmission electron microscopy, we report that Arg177 and Asp159 from the dog PrP slow the LLPS of full-length human PrPC, shifting the equilibrium phase boundary to higher protein concentrations and inhibit amyloid formation of the human protein. In sharp contrast, His177 and Asn159 from the human PrP enhance the LLPS of full-length dog PrPC, shifting the equilibrium phase boundary to lower protein concentrations, and promote fibril formation of the canid protein. Collectively, these results demonstrate how LLPS and amyloid formation of PrP are inhibited by a single residue Arg177 or Asp159 associated with prion disease resistance, and how LLPS and fibril formation of PrP are promoted by a single residue His177 or Asn159. Therefore, Arg177/His177 and Asp159/Asn159 are key residues in modulating PrPC liquid-phase condensation.
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Affiliation(s)
- Xiang-Ning Li
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Yuan Gao
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Yang Li
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Jin-Xu Yin
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Chuan-Wei Yi
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Han-Ye Yuan
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Jun-Jie Huang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Li-Qiang Wang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China; Wuhan University Shenzhen Research Institute, Shenzhen, China
| | - Jie Chen
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Yi Liang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China; Wuhan University Shenzhen Research Institute, Shenzhen, China.
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Shahbazi Toloun SS, Pishkar L. Study of the prostate-specific antigen–aptamer stability in the PSA–aptamer-single wall carbon nanotube assembly by docking and molecular dynamics simulation. MOLECULAR SIMULATION 2021. [DOI: 10.1080/08927022.2021.1932874] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
| | - Leila Pishkar
- Department of Biology, Islamshahr Branch, Islamic Azad University, Islamshahr, Iran
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Harrathi C, Fernández-Borges N, Eraña H, Elezgarai SR, Venegas V, Charco JM, Castilla J. Insights into the Bidirectional Properties of the Sheep-Deer Prion Transmission Barrier. Mol Neurobiol 2018; 56:5287-5303. [PMID: 30592012 PMCID: PMC6614146 DOI: 10.1007/s12035-018-1443-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 11/30/2018] [Indexed: 02/06/2023]
Abstract
The large chronic wasting disease (CWD)-affected cervid population in the USA and Canada, and the risk of the disease being transmitted to humans through intermediate species, is a highly worrying issue that is still poorly understood. In this case, recombinant protein misfolding cyclic amplification was used to determine, in vitro, the relevance of each individual amino acid on cross-species prion transmission. Others and we have found that the β2-α2 loop is a key modulator of transmission barriers between species and markedly influences infection by sheep scrapie, bovine spongiform encephalopathy (BSE), or elk CWD. Amino acids that differentiate ovine and deer normal host prion protein (PrPC) and associated with structural rigidity of the loop β2-α2 (S173N, N177T) appear to confer resistance to some prion diseases. However, addition of methionine at codon 208 together with the previously described rigid loop substitutions seems to hide a key in this species barrier, as it makes sheep recombinant prion protein highly susceptible to CWD-induced misfolding. These studies indicate that interspecies prion transmission is not only governed just by the β2-α2 loop amino acid sequence but also by its interactions with the α3-helix as shown by substitution I208M. Transmissible spongiform encephalopathies, characterized by long incubation periods and spongiform changes associated with neuronal loss in the brain, have been described in several mammalian species appearing either naturally (scrapie in sheep and goats, bovine spongiform encephalopathy in cattle, chronic wasting disease in cervids, Creutzfeldt-Jakob disease in humans) or by experimental transmission studies (scrapie in mice and hamsters). Much of the pathogenesis of the prion diseases has been determined in the last 40 years, such as the etiological agent or the fact that prions occur as different strains that show distinct biological and physicochemical properties. However, there are many unanswered questions regarding the strain phenomenon and interspecies transmissibility. To assess the risk of interspecies transmission between scrapie and chronic wasting disease, an in vitro prion propagation method has been used. This technique allows to predict the amino acids preventing the transmission between sheep and deer prion diseases.
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Affiliation(s)
- Chafik Harrathi
- CIC bioGUNE, Parque tecnológico de Bizkaia, 48160, Derio, Bizkaia, Spain
| | | | - Hasier Eraña
- CIC bioGUNE, Parque tecnológico de Bizkaia, 48160, Derio, Bizkaia, Spain
| | - Saioa R Elezgarai
- CIC bioGUNE, Parque tecnológico de Bizkaia, 48160, Derio, Bizkaia, Spain
| | - Vanessa Venegas
- CIC bioGUNE, Parque tecnológico de Bizkaia, 48160, Derio, Bizkaia, Spain
| | - Jorge M Charco
- CIC bioGUNE, Parque tecnológico de Bizkaia, 48160, Derio, Bizkaia, Spain
| | - Joaquín Castilla
- CIC bioGUNE, Parque tecnológico de Bizkaia, 48160, Derio, Bizkaia, Spain. .,IKERBASQUE, Basque Foundation for Science, 48011, Bilbao, Bizkaia, Spain.
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Eisold A, Labudde D. Detailed Analysis of 17β-Estradiol-Aptamer Interactions: A Molecular Dynamics Simulation Study. Molecules 2018; 23:molecules23071690. [PMID: 29997341 PMCID: PMC6100600 DOI: 10.3390/molecules23071690] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 07/06/2018] [Accepted: 07/09/2018] [Indexed: 12/16/2022] Open
Abstract
Micro-pollutants such as 17β-Estradiol (E2) have been detected in different water resources and their negative effects on the environment and organisms have been observed. Aptamers are established as a possible detection tool, but the underlying ligand binding is largely unexplored. In this study, a previously described 35-mer E2-specific aptamer was used to analyse the binding characteristics between E2 and the aptamer with a MD simulation in an aqueous medium. Because there is no 3D structure information available for this aptamer, it was modeled using coarse-grained modeling method. The E2 ligand was positioned inside a potential binding area of the predicted aptamer structure, the complex was used for an 25 ns MD simulation, and the interactions were examined for each time step. We identified E2-specific bases within the interior loop of the aptamer and also demonstrated the influence of frequently underestimated water-mediated hydrogen bonds. The study contributes to the understanding of the behavior of ligands binding with aptamer structure in an aqueous solution. The developed workflow allows generating and examining further appealing ligand-aptamer complexes.
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Affiliation(s)
- Alexander Eisold
- Faculty of Applied Computer and Biosciences, University of Applied Sciences Mittweida, Technikumplatz 17, 09648 Mittweida, Germany.
- Institute for Organic Chemistry, Technische Universität Bergakademie Freiberg, Leipziger Straße 29, 09599 Freiberg, Germany.
| | - Dirk Labudde
- Faculty of Applied Computer and Biosciences, University of Applied Sciences Mittweida, Technikumplatz 17, 09648 Mittweida, Germany.
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In Vitro Approach To Identify Key Amino Acids in Low Susceptibility of Rabbit Prion Protein to Misfolding. J Virol 2017; 91:JVI.01543-17. [PMID: 28978705 DOI: 10.1128/jvi.01543-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 09/22/2017] [Indexed: 01/10/2023] Open
Abstract
Prion diseases, or transmissible spongiform encephalopathies (TSEs), are a group of rare progressive neurodegenerative disorders caused by an abnormally folded prion protein (PrPSc). This is capable of transforming the normal cellular prion protein (PrPC) into new infectious PrPSc Interspecies prion transmissibility studies performed by experimental challenge and the outbreak of bovine spongiform encephalopathy that occurred in the late 1980s and 1990s showed that while some species (sheep, mice, and cats) are readily susceptible to TSEs, others are apparently resistant (rabbits, dogs, and horses) to the same agent. To study the mechanisms of low susceptibility to TSEs of certain species, the mouse-rabbit transmission barrier was used as a model. To identify which specific amino acid residues determine high or low susceptibility to PrPSc propagation, protein misfolding cyclic amplification (PMCA), which mimics PrPC-to-PrPSc conversion with accelerated kinetics, was used. This allowed amino acid substitutions in rabbit PrP and accurate analysis of misfolding propensities. Wild-type rabbit recombinant PrP could not be misfolded into a protease-resistant self-propagating isoform in vitro despite seeding with at least 12 different infectious prions from diverse origins. Therefore, rabbit recombinant PrP mutants were designed to contain every single amino acid substitution that distinguishes rabbit recombinant PrP from mouse recombinant PrP. Key amino acid residue substitutions were identified that make rabbit recombinant PrP susceptible to misfolding, and using these, protease-resistant misfolded recombinant rabbit PrP was generated. Additional studies characterized the mechanisms by which these critical amino acid residue substitutions increased the misfolding susceptibility of rabbit PrP.IMPORTANCE Prion disorders are invariably fatal, untreatable diseases typically associated with long incubation periods and characteristic spongiform changes associated with neuronal loss in the brain. Development of any treatment or preventative measure is dependent upon a detailed understanding of the pathogenesis of these diseases, and understanding the mechanism by which certain species appear to be resistant to TSEs is critical. Rabbits are highly resistant to naturally acquired TSEs, and even under experimental conditions, induction of clinical disease is not easy. Using recombinant rabbit PrP as a model, this study describes critical molecular determinants that confer this high resistance to transmissible spongiform encephalopathies.
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Nisha J, Shanthi V. Characterization of Ofloxacin Interaction with Mutated (A91V) Quinolone Resistance Determining Region of DNA Gyrase in Mycobacterium Leprae through Computational Simulation. Cell Biochem Biophys 2017; 76:125-134. [PMID: 28822069 DOI: 10.1007/s12013-017-0822-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Accepted: 08/04/2017] [Indexed: 02/04/2023]
Abstract
Mycobacterium leprae, the causal agent of leprosy is non-cultivable in vitro. Thus, the assessment of antibiotic activity against Mycobacterium leprae depends primarily upon the time-consuming mouse footpad system. The GyrA protein of Mycobacterium leprae is the target of the antimycobacterial drug, Ofloxacin. In recent times, the GyrA mutation (A91V) has been found to be resistant to Ofloxacin. This phenomenon has necessitated the development of new, long-acting antimycobacterial compounds. The underlying mechanism of drug resistance is not completely known. Currently, experimentally crystallized GyrA-DNA-OFLX models are not available for highlighting the binding and mechanism of Ofloxacin resistance. Hence, we employed computational approaches to characterize the Ofloxacin interaction with both the native and mutant forms of GyrA complexed with DNA. Binding energy measurements obtained from molecular docking studies highlights hydrogen bond-mediated efficient binding of Ofloxacin to Asp47 in the native GyrA-DNA complex in comparison with that of the mutant GyrA-DNA complex. Further, molecular dynamics studies highlighted the stable binding of Ofloxacin with native GyrA-DNA complex than with the mutant GyrA-DNA complex. This mechanism provided a plausible reason for the reported, reduced effect of Ofloxacin to control leprosy in individuals with the A91V mutation. Our report is the first of its kind wherein the basis for the Ofloxacin drug resistance mechanism has been explored with the help of ternary Mycobacterium leprae complex, GyrA-DNA-OFLX. These structural insights will provide useful information for designing new drugs to target the Ofloxacin-resistant DNA gyrase.
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Affiliation(s)
- J Nisha
- Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, 632014, Tamil Nadu, India
| | - V Shanthi
- Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, 632014, Tamil Nadu, India.
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Ahmad A, Burns CS, Fink AL, Uversky VN. Peculiarities of copper binding to alpha-synuclein. J Biomol Struct Dyn 2016; 29:825-42. [PMID: 22208282 DOI: 10.1080/073911012010525023] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Heavy metals have been implicated as the causative agents for the pathogenesis of the most prevalent neurodegenerative disease. Various mechanisms have been proposed to explain the toxic effects of metals ranging from metal-induced oxidation of protein to metal-induced changes in the protein conformation. Aggregation of a-synuclein is implicated in Parkinson's disease (PD), and various metals, including copper, constitute a prominent group of alpha-synuclein aggregation enhancers. In this study, we have systematically characterized the a-synuclein-Cu21 binding sites and analyzed the possible role of metal binding in a-synuclein fibrillation using a set of biophysical techniques, such as electron paramagnetic resonance (EPR), electron spin-echo envelope modulation (ESEEM), circular dichroism (CD), and size exclusion chromatography (SEC). Our analyses indicated that a-synuclein possesses at least two binding sites for Cu21. We have been able to locate one of the binding sites in the N-terminal region. Furthermore, based on the EPR studies of model peptides and Beta-synuclein, we concluded that the suspected His residue did not appear to participate in strong Cu21 binding.
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Affiliation(s)
- Atta Ahmad
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California, USA.
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Qing LL, Zhao H, Liu LL. Progress on low susceptibility mechanisms of transmissible spongiform encephalopathies. DONG WU XUE YAN JIU = ZOOLOGICAL RESEARCH 2015; 35:436-45. [PMID: 25297084 DOI: 10.13918/j.issn.2095-8137.2014.5.436] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Transmissible spongiform encephalopathies (TSEs), also known as prion diseases, are a group of fatal neurodegenerative diseases detected in a wide range of mammalian species. The "protein-only" hypothesis of TSE suggests that prions are transmissible particles devoid of nucleic acid and the primary pathogenic event is thought to be the conversion of cellular prion protein (PrP(C)) into the disease-associated isoform (PrP(Sc)). According to susceptibility to TSEs, animals can be classified into susceptible species and low susceptibility species. In this review we focus on several species with low susceptibility to TSEs: dogs, rabbits, horses and buffaloes. We summarize recent studies into the characteristics of low susceptibility regarding protein structure, and biochemical and genetic properties.
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Affiliation(s)
- Li-Li Qing
- Laboratory of Conservation and Utilization of Bio-resources, Yunnan University, Kunming 650091, China
| | - Hui Zhao
- Laboratory of Conservation and Utilization of Bio-resources, Yunnan University, Kunming 650091, China.
| | - Lin-Lin Liu
- Laboratory of Conservation and Utilization of Bio-resources, Yunnan University, Kunming 650091, China
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Doss CGP, Rajith B, Rajasekaran R, Srajan J, Nagasundaram N, Debajyoti C. In silico analysis of prion protein mutants: a comparative study by molecular dynamics approach. Cell Biochem Biophys 2014; 67:1307-18. [PMID: 23723004 DOI: 10.1007/s12013-013-9663-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Polymorphisms in the human prion proteins lead to amino acid substitutions by the conversion of PrPC to PrPSc and amyloid formation, resulting in prion diseases such as familial Creutzfeldt-Jakob disease, Gerstmann-Straussler-Scheinker disease and fatal familial insomnia. Cation-π interaction is a non-covalent binding force that plays a significant role in protein stability. Here, we employ a novel approach by combining various in silico tools along with molecular dynamics simulation to provide structural and functional insight into the effect of mutation on the stability and activity of mutant prion proteins. We have investigated impressions of prevalent mutations including 1E1S, 1E1P, 1E1U, 1E1P, 1FKC and 2K1D on the human prion proteins and compared them with wild type. Structural analyses of the models were performed with the aid of molecular dynamics simulation methods. According to our results, frequently occurred mutations were observed in conserved sequences of human prion proteins and the most fluctuation values appear in the 2K1D mutant model at around helix 4 with residues ranging from 190 to 194. Our observations in this study could help to further understand the structural stability of prion proteins.
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Affiliation(s)
- C George Priya Doss
- Medical Biotechnology Division, School of Biosciences and Technology, VIT University, Vellore, 632014, Tamil Nadu, India,
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Rustamov IR, Dyatlov VA, Grebeneva TA, Dyatlov AV, Zaitsev VV, Maleev VI. Polycyanoacrylate porous material for bone tissue substitution. J Mater Chem B 2014; 2:4310-4317. [PMID: 32261569 DOI: 10.1039/c4tb00554f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A proof of concept study has been conducted for the design of a porous biodegradable material containing nanocapsules and two actives with independent release-bimodal drug-eluting implants. Completely safe synthetic material free from risk of prion and virus contamination was tested in vivo, and a method for controlling the rate of biodegradation of poly-2-cyanoacrylic polymer was developed. Novel perfluorinated 2-cyanoacrylic esters have been applied for the chemical modification of polyethyl-2-cyanoacrlylate copolymers. Internal imide-cycle formation has been used to retard the rate of enzymatic hydrolysis of the 2-cyanoacrylic copolymer main chain.
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Affiliation(s)
- I R Rustamov
- D. Mendeleev University of Chemical Technology of Russia, Russia
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Yuan Z, Zhao D, Yang L. Decipher the mechanisms of rabbit's low susceptibility to prion infection. Acta Biochim Biophys Sin (Shanghai) 2013; 45:899-903. [PMID: 24041958 DOI: 10.1093/abbs/gmt093] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Rabbits have low susceptibility to prion infection. Studies on prion protein (PrP) from animal species of different susceptibility to prion diseases identified key amino acid residues, specific motif, and special features in rabbit prion protein (RaPrP(C)) that contribute to the stability of rabbit PrP(C) and low susceptibility to prion infection. However, there is no evidence showing that rabbits are completely resistant to prion diseases. It has been reported that the rabbit prion could be generated in vitro through protein misfolding cyclic amplification and proved to be infectious and transmissible. Here, we reviewed studies on rabbit-specific PrP structures and features in relation to rabbit's low susceptibility to prion infection.
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Affiliation(s)
- Zhen Yuan
- State Key Laboratories for Agrobiotechnology, Key Lab of Animal Epidemiology and Zoonosis, Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
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Coimbra JT, Sousa SF, Fernandes PA, Rangel M, Ramos MJ. Biomembrane simulations of 12 lipid types using the general amber force field in a tensionless ensemble. J Biomol Struct Dyn 2013; 32:88-103. [DOI: 10.1080/07391102.2012.750250] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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De Simone A, Stanzione F, Marasco D, Vitagliano L, Esposito L. The intrinsic stability of the human prion β-sheet region investigated by molecular dynamics. J Biomol Struct Dyn 2013; 31:441-52. [DOI: 10.1080/07391102.2012.703070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Fernández-Borges N, Chianini F, Eraña H, Vidal E, Eaton SL, Pintado B, Finlayson J, Dagleish MP, Castilla J. Naturally prion resistant mammals: a utopia? Prion 2012; 6:425-9. [PMID: 22954650 DOI: 10.4161/pri.22057] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Each known abnormal prion protein (PrP (Sc) ) is considered to have a specific range and therefore the ability to infect some species and not others. Consequently, some species have been assumed to be prion disease resistant as no successful natural or experimental challenge infections have been reported. This assumption suggested that, independent of the virulence of the PrP (Sc) strain, normal prion protein (PrP (C) ) from these 'resistant' species could not be induced to misfold. Numerous in vitro and in vivo studies trying to corroborate the unique properties of PrP (Sc) have been undertaken. The results presented in the article "Rabbits are not resistant to prion infection" demonstrated that normal rabbit PrP (C) , which was considered to be resistant to prion disease, can be misfolded to PrP (Sc) and subsequently used to infect and transmit a standard prion disease to leporids. Using the concept of species resistance to prion disease, we will discuss the mistake of attributing species specific prion disease resistance based purely on the absence of natural cases and incomplete in vivo challenges. The BSE epidemic was partially due to an underestimation of species barriers. To repeat this error would be unacceptable, especially if present knowledge and techniques can show a theoretical risk. Now that the myth of prion disease resistance has been refuted it is time to re-evaluate, using the new powerful tools available in modern prion laboratories, whether any other species could be at risk.
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Matos KS, da Cunha EF, da Silva Gonçalves A, Wilter A, Kuča K, França TC, Ramalho TC. First principles calculations of thermodynamics and kinetic parameters and molecular dynamics simulations of acetylcholinesterase reactivators: can mouse data provide new insights into humans? J Biomol Struct Dyn 2012; 30:546-58. [DOI: 10.1080/07391102.2012.687521] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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Abstract
The small ubiquitin-like modifier (SUMO) proteins are a kind of proteins that can be attached to a series of proteins. The sumoylation of protein is an important posttranslational modification. Thus, the prediction of the sumoylation site of a given protein is significant. Here we employed a combined method to perform this task. We predicted the sumoylation site of a protein by a two-staged procedure. At the first stage, whether a protein would be sumoylated was predicted; whereas at the second stage, the sumoylation sites of the protein were predicted if it was determined to be modified by SUMO at the first stage. At the first stage, we encoded a protein with protein families (PFAM) and trained the predictor with nearest network algorithm (NNA); at the second stage, we encoded nonapeptides (peptides that contain nine residues) of the protein containing the lysine residues, with Amino Acid Index, and trained the predictor with NNA. The predictor was tested by the k-fold cross-validation method. The highest accuracy of the second-staged predictor was 99.55% when 12 features were incorporated in the predictor. The corresponding Matthews Correlation Coefficient was 0.7952. These results indicate that the method is a promising tool to predict the sumoylation site of a protein. At last, the features used in the predictor are discussed. The software is available at request.
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Affiliation(s)
- YuDong Cai
- Institute of System Biology, Shanghai University, 99 Shangda Road, Shanghai, 200244, China.
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Semighini EP, Resende JA, de Andrade P, Morais PAB, Carvalho I, Taft CA, Silva CHTP. Using computer-aided drug design and medicinal chemistry strategies in the fight against diabetes. J Biomol Struct Dyn 2011; 28:787-96. [PMID: 21294589 DOI: 10.1080/07391102.2011.10508606] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The aim of this work is to present a simple, practical and efficient protocol for drug design, in particular Diabetes, which includes selection of the illness, good choice of a target as well as a bioactive ligand and then usage of various computer aided drug design and medicinal chemistry tools to design novel potential drug candidates in different diseases. We have selected the validated target dipeptidyl peptidase IV (DPP-IV), whose inhibition contributes to reduce glucose levels in type 2 diabetes patients. The most active inhibitor with complex X-ray structure reported was initially extracted from the BindingDB database. By using molecular modification strategies widely used in medicinal chemistry, besides current state-of-the-art tools in drug design (including flexible docking, virtual screening, molecular interaction fields, molecular dynamics, ADME and toxicity predictions), we have proposed 4 novel potential DPP-IV inhibitors with drug properties for Diabetes control, which have been supported and validated by all the computational tools used herewith.
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Affiliation(s)
- Evandro P Semighini
- Departamento de Ciencias Farmaceuticas, Faculdade de Ciencias Farmaceuticas de Ribeirao Preto, Universidade de Sao Paulo, Av. do Cafe, s/n, Monte Alegre, 14040-903, Ribeirao Preto-SP, Brazil
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Chang TT, Sun MF, Chen HY, Tsai FJ, Fisher M, Lin JG, Chen CYC. Screening from the world's largest TCM database against H1N1 virus. J Biomol Struct Dyn 2011; 28:773-86. [PMID: 21294588 DOI: 10.1080/07391102.2011.10508605] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The swine influenza virus (H1N1) 2009 pandemic highlights the importance of having effective anti-viral strategies. Recently, oseltamivir (Tamiflu) resistant influenza viruses are identified; which further emphasizes the urgency in developing new antiviral agents. In influenza virus replication cycle, viral surface glycoprotein, hemagglutinin, is responsible for viral entry into host cells. Hence, a potentially effective antiviral strategy is to inhibit viral entry mechanism. To develop novel antiviral agent that inhibits viral entry, we analyzed 20,000 traditional Chinese medicine (TCM) ingredients in hemagglutinin subtype H1 sialic acid binding site found on H1N1 virus. We then performed molecular dynamics simulations to investigate receptor-ligand interaction of the candidates obtained from docking. Here, we report three TCM derivatives that have high binding affinities to H1 sialic acid binding site residues based on structure-based calculations. The top three derivatives, xylopine_2, rosmaricine_14 and rosmaricine_15, all have an amine group that interact with Glu83 and a pyridinium group that interact with Asp103. Molecular dynamics simulations show that these derivatives form strong hydrogen bonding with Glu83 but interact transiently with Asp103. We therefore suggest that an enhanced hemagglutinin inhibitor, based on our scaffold, should be designed to bind both Glu83 and Asp103 with high affinity.
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Affiliation(s)
- Tung-Ti Chang
- Laboratory of Computational and Systems Biology, School of Chinese Medicine, China Medical University, Taichung, 40402, Taiwan
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19
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Xu X, Su J, Chen W, Wang C. Thermal stability and unfolding pathways of Sso7d and its mutant F31A: insight from molecular dynamics simulation. J Biomol Struct Dyn 2011; 28:717-27. [PMID: 21294584 DOI: 10.1080/07391102.2011.10508601] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The thermo-stability and unfolding behaviors of a small hyperthermophilic protein Sso7d as well as its single-point mutation F31A are studied by molecular dynamics simulation at temperatures of 300 K, 371 K and 500 K. Simulations at 300 K show that the F31A mutant displays a much larger flexibility than the wild type, which implies that the mutation obviously decreases the protein's stability. In the simulations at 371 K, although larger fluctuations were observed, both of these two maintain their stable conformations. High temperature simulations at 500 K suggest that the unfolding of these two proteins evolves along different pathways. For the wild-type protein, the C-terminal alpha-helix is melted at the early unfolding stage, whereas it is destroyed much later in the unfolding process of the F31A mutant. The results also show that the mutant unfolds much faster than its parent protein. The deeply buried aromatic cluster in the F31A mutant dissociates quickly relative to the wild-type protein at high temperature. Besides, it is found that the triple-stranded antiparallel β-sheet in the wild-type protein plays an important role in maintaining the stability of the entire structure.
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Affiliation(s)
- Xianjin Xu
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China
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20
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21
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Majumder R, Roy S, Thakur AR. Molecular Modeling and Molecular Dynamics Simulation Studies of Delta-Notch Complex. J Biomol Struct Dyn 2011; 29:297-310. [DOI: 10.1080/07391102.2011.10507386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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22
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Behmard E, Abdolmaleki P, Asadabadi EB, Jahandideh S. Prevalent Mutations of Human Prion Protein: A Molecular Modeling and Molecular Dynamics Study. J Biomol Struct Dyn 2011; 29:379-89. [DOI: 10.1080/07391102.2011.10507392] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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23
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Oliveira AA, Rennó MN, de Matos CAS, Bertuzzi MD, Ramalho TC, Fraga CA, França TCC. Molecular Modeling Studies ofYersinia pestisDihydrofolate Reductase. J Biomol Struct Dyn 2011; 29:351-67. [DOI: 10.1080/07391102.2011.10507390] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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24
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Jani V, Sonavane UB, Joshi R. Microsecond scale replica exchange molecular dynamic simulation of villin headpiece: an insight into the folding landscape. J Biomol Struct Dyn 2011; 28:845-60. [PMID: 21469746 DOI: 10.1080/07391102.2011.10508612] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Reaching the experimental time scale of millisecond is a grand challenge for protein folding simulations. The development of advanced Molecular Dynamics techniques like Replica Exchange Molecular Dynamics (REMD) makes it possible to reach these experimental timescales. In this study, an attempt has been made to reach the multi microsecond simulation time scale by carrying out folding simulations on a three helix bundle protein, Villin, by combining REMD and Amber United Atom model. Twenty replicas having different temperatures ranging from 295 K to 390 K were simulated for 1.5 µs each. The lowest Root Mean Square Deviation (RMSD) structure of 2.5 Å was obtained with respect to native structure (PDB code 1VII), with all the helices formed. The folding population landscapes were built using segment-wise RMSD and Principal Components as reaction coordinates. These analyses suggest the two-stage folding for Villin. The combination of REMD and Amber United Atom model may be useful to understand the folding mechanism of various fast folding proteins.
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Affiliation(s)
- Vinod Jani
- Bioinformatics Team, Scientific and Engineering Computing Group, Centre for Development of Advanced Computing, Pune University Campus, Ganeshkhind, Pune - 411007, Maharashtra, India
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25
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Su JG, Xu XJ, Li CH, Chen WZ, Wang CX. An Analysis of the Influence of Protein Intrinsic Dynamical Properties on its Thermal Unfolding Behavior. J Biomol Struct Dyn 2011; 29:105-21. [DOI: 10.1080/07391102.2011.10507377] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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26
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Purohit R, Rajendran V, Sethumadhavan R. Studies on Adaptability of Binding Residues Flap Region of TMC-114 Resistance HIV-1 Protease Mutants. J Biomol Struct Dyn 2011; 29:137-52. [DOI: 10.1080/07391102.2011.10507379] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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27
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Zhang J, Gao DY, Yearwood J. A novel canonical dual computational approach for prion AGAAAAGA amyloid fibril molecular modeling. J Theor Biol 2011; 284:149-57. [PMID: 21723301 DOI: 10.1016/j.jtbi.2011.06.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Revised: 06/15/2011] [Accepted: 06/17/2011] [Indexed: 12/22/2022]
Abstract
Many experimental studies have shown that the prion AGAAAAGA palindrome hydrophobic region (113-120) has amyloid fibril forming properties and plays an important role in prion diseases. However, due to the unstable, noncrystalline and insoluble nature of the amyloid fibril, to date structural information on AGAAAAGA region (113-120) has been very limited. This region falls just within the N-terminal unstructured region PrP (1-123) of prion proteins. Traditional X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy experimental methods cannot be used to get its structural information. Under this background, this paper introduces a novel approach of the canonical dual theory to address the 3D atomic-resolution structure of prion AGAAAAGA amyloid fibrils. The novel and powerful canonical dual computational approach introduced in this paper is for the molecular modeling of prion AGAAAAGA amyloid fibrils, and that the optimal atomic-resolution structures of prion AGAAAAGA amyloid fibils presented in this paper are useful for the drive to find treatments for prion diseases in the field of medicinal chemistry. Overall, this paper presents an important method and provides useful information for treatments of prion diseases.
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Affiliation(s)
- Jiapu Zhang
- Centre in Informatics and Applied Optimization, Graduate School of Sciences, Informatics Technology and Engineering, University of Ballarat, Mount Helen, VIC 3353, Australia.
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28
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Optimal atomic-resolution structures of prion AGAAAAGA amyloid fibrils. J Theor Biol 2011; 279:17-28. [DOI: 10.1016/j.jtbi.2011.02.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2010] [Revised: 02/05/2011] [Accepted: 02/16/2011] [Indexed: 11/20/2022]
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29
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Zhang J, Liu DD. Molecular Dynamics Studies on the Structural Stability of Wild-type Dog Prion Protein. J Biomol Struct Dyn 2011; 28:861-9. [DOI: 10.1080/07391102.2011.10508613] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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30
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Lin CH, Chang TT, Sun MF, Chen HY, Tsai FJ, Chang KL, Fisher M, Chen CYC. Potent inhibitor design against H1N1 swine influenza: structure-based and molecular dynamics analysis for M2 inhibitors from traditional Chinese medicine database. J Biomol Struct Dyn 2011; 28:471-82. [PMID: 21142218 DOI: 10.1080/07391102.2011.10508589] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The rapid spread of influenza virus subtype H1N1 poses a great threat to million lives worldwide. To search for new anti-influenza compounds, we performed molecular docking and molecular dynamics simulation to identify potential traditional Chinese medicine (TCM) constituents that could block influenza M2 channel activity. Quinic acid, genipin, syringic acid, cucurbitine, fagarine, and methyl isoferulate all have extremely well docking results as compared to control amantadine. Further de novo drug design suggests that derivatives of genipin and methyl isoferulate could have enhanced binding affinity towards M2 channel. Selected molecular dynamics simulations of M2-derivative complexes show stable hydrogen bond interactions between the derivatives and M2 residues, Ser10 and Ala9. To our best knowledge, this is the first study on the anti-viral activity of the above listed TCM compounds.
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Affiliation(s)
- Chia-Hui Lin
- Department of Chinese Medicine, China Medical University Hospital, Taiwan
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31
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Zhou ZL, Zhao JH, Liu HL, Wu JW, Liu KT, Chuang CK, Tsai WB, Ho Y. The Possible Structural Models for Polyglutamine Aggregation: A Molecular Dynamics Simulations Study. J Biomol Struct Dyn 2011; 28:743-58. [DOI: 10.1080/07391102.2011.10508603] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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32
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Olmez EO, Alakent B. Alpha7 Helix Plays an Important Role in the Conformational Stability of PTP1B. J Biomol Struct Dyn 2011; 28:675-93. [DOI: 10.1080/07391102.2011.10508599] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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33
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Roy S, Thakur AR. Two models of Smad4 and Hoxa9 Complex are Proposed: Structural and Interactional Perspective. J Biomol Struct Dyn 2011; 28:729-42. [DOI: 10.1080/07391102.2011.10508602] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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34
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Zhao Y, Gong Z, Xiao Y. Improvements of the Hierarchical Approach for Predicting RNA Tertiary Structure. J Biomol Struct Dyn 2011; 28:815-26. [DOI: 10.1080/07391102.2011.10508609] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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35
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Guimarães AP, Oliveira AA, da Cunha EFF, Ramalho TC, França TCC. Design of New Chemotherapeutics Against the Deadly Anthrax Disease. Docking and Molecular Dynamics studies of Inhibitors Containing Pyrrolidine and Riboamidrazone Rings on Nucleoside Hydrolase fromBacillus anthracis. J Biomol Struct Dyn 2011; 28:455-69. [DOI: 10.1080/07391102.2011.10508588] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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36
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Chakrabarti B, Bairagya HR, Mallik P, Mukhopadhyay BP, Bera AK. An Insight to Conserved Water Molecular Dynamics of Catalytic and Structural Zn+2ions in Matrix Metalloproteinase 13 of Human. J Biomol Struct Dyn 2011; 28:503-16. [DOI: 10.1080/07391102.2011.10508591] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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37
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Lee HM, Jin B, Han SW, Kim SK. Conformational analysis of genotoxic benzo[a]pyrene-7,8-dione-duplex DNA adducts using a molecular dynamics method (II). J Biomol Struct Dyn 2011; 28:421-30. [PMID: 20919757 DOI: 10.1080/07391102.2010.10507371] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The conformations of the benzo[a]pyrene-7,8-quinone (BPQ) modified oligonucleotide were investigated using molecular dynamic simulation. In the initial structures, the central guanine base was modified with BPQ resulting in the formation of four structurally distinguishable 10-(N2-deoxyguanosyl)-9,10-dihydro-9-hydroxy benzo[a]pyrene-7,8-dione adducts (BPQ-G3,4). Each of the oligonucleotide adduct consisted of two conformers, namely syn and anti conformations, depending on the rotation around the glycosidic bond between BPQ and the guanine base. The results revealed that the BPQ moiety was located in the major groove for all four syn conformers. The relative energies of these conformers were high, and the backbone largely deviated from the B-form. On the other hand, BPQ was located in the minor groove with relatively low energies, and backbone was retained in all of the anti conformer cases. The most conceivable BPQ-modified double stranded oligonucleotide structure was proposed from the energy calculation and the structural analysis.
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Affiliation(s)
- Hyun Mee Lee
- Department of Chemistry, Yeungnam University, Daedong, Gyeongsan City, Gyeong-buk, 712-749, Republic of Korea
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38
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Gong Z, Xiao Y, Xiao Y. RNA stability under different combinations of amber force fields and solvation models. J Biomol Struct Dyn 2011; 28:431-41. [PMID: 20919758 DOI: 10.1080/07391102.2010.10507372] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The proper matching of force field and solvent is critical to obtain correct result in molecular dynamics simulation of bio-molecules. This problem has been intensively investigated for protein but not for RNA yet. In this paper, we use standard molecular dynamics and replica exchange molecular dynamics to take a series of tests on the RNA stability under different combinations of Amber force field parameters (ff98, ff99 and ff99bsc0) and the general Born implicit solvent models (igb1, igb2 and igb5). It is found that only ff98 and ff99bsc0 with igb1 can keep the native conformations of RNA hairpin and duplex. Our results suggest that ff98 plus igb1 may be reasonable choice for molecular dynamics simulation of RNA dynamics.
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Affiliation(s)
- Zhou Gong
- Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
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39
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Zhang J. Comparison studies of the structural stability of rabbit prion protein with human and mouse prion proteins. J Theor Biol 2011; 269:88-95. [DOI: 10.1016/j.jtbi.2010.10.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2010] [Revised: 09/07/2010] [Accepted: 10/15/2010] [Indexed: 11/16/2022]
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40
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Zhong L. Exposure of Hydrophobic Core in Human Prion Protein Pathogenic Mutant H187R. J Biomol Struct Dyn 2010; 28:355-61. [DOI: 10.1080/07391102.2010.10507365] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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41
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Chang TT, Huang HJ, Lee KJ, Yu HW, Chen HY, Tsai FJ, Sun MF, Chen CYC. Key Features for Designing Phosphodiesterase-5 Inhibitors. J Biomol Struct Dyn 2010; 28:309-21. [DOI: 10.1080/07391102.2010.10507361] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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42
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Poddar NK, Ansari ZA, Singh RKB, Movahedi AAM, Ahmad F. Effect of Oligosaccharides and their Monosaccharide Mixtures on the Stability of Proteins: A Scaled Particle Study. J Biomol Struct Dyn 2010; 28:331-41. [DOI: 10.1080/07391102.2010.10507363] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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43
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Cao Z, Liu L, Wang J. Effects of pH and Temperature on the Structural and Thermodynamic Character of a-syn12 Peptide in Aqueous Solution. J Biomol Struct Dyn 2010; 28:343-53. [DOI: 10.1080/07391102.2010.10507364] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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44
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Huang HJ, Lee KJ, Yu HW, Chen HY, Tsai FJ, Chen CYC. A novel strategy for designing the selective PPAR agonist by the "sum of activity" model. J Biomol Struct Dyn 2010; 28:187-200. [PMID: 20645652 DOI: 10.1080/07391102.2010.10507352] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Peroxisome proliferator-activated receptors alpha, delta and gamma are a collection of ligand-activated transcription factors crucial in lipid and glucose homeostasis. The involvement of these receptors in lipid metabolism makes them perfect therapeutic target for treating obesity and stroke. In this study, 'sum of activity' model was employed to design multi-target agonists. We used a new strategy to design agonists that fit both alpha and delta but not gamma, to avoid side effect. The CoMFA and CoMSIA models were used to explore the pharmacophore features by constructing three individual models: (a) alpha-model, (b) delta-model and (c) gamma-model, and two sum models: (d) alpha, delta- model, and (e) alpha, delta and gamma-model. The CoMFA model yielded a significant cross validation value, q(2), of 0.729 and non-cross validation value, r(2), of 0.933 in the alpha, delta-model. The CoMSIA studies yielded the best predictive models with q(2) of 0.622 in A+S and with r(2) of 0.911 in the alpha, delta-model. Finally, we proposed that distinct features shown in models (a), (b), (d) but not (c) and (e) should be accounted in designing weight-controlling drugs.
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Affiliation(s)
- Hung-Jin Huang
- Laboratory of Computational and Systems Biology, School of Chinese Medicine, China Medical University, Taichung, 40402, Taiwan, ROC
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45
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Nasiri R, Bahrami H, Zahedi M, Moosavi-Movahedi AA, Sattarahmady N. A theoretical elucidation of glucose interaction with HSA's domains. J Biomol Struct Dyn 2010; 28:211-26. [PMID: 20645654 DOI: 10.1080/07391102.2010.10507354] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The interaction of different domains belonging to Human Serum Albumin (HSA) with open form of glucose have been investigated using molecular dynamics simulation methods. Applying docking, primary structures involving interaction of some residues with glucose have been obtained. Subsequently, equilibrium geometries at 300 K and minimum geometries have been determined for each of aforementioned structures by employing MD simulation and simulated annealing. The stability of species has been evaluated using a SAWSA v2.0 model. Ultimately, NBO analysis has been carried out to specify possible hydrogen bonding regarding the HSA interaction with glucose. Results obtained show that glucose can interact with Lys195, Lys199, and Glu153. In these interactions, each lysine forms an H-bonding with glucose. The H-bonding is obtained by stretching of N-H bond belonging to NH(3)(+) group of lysine along an oxygen atom of glucose. In addition, the above mentioned lysines are protonated, and there is an electrostatic interaction between glucose with Lys195 or Lys199. In addition, an H-bonding is formed between O atom of -COO group belonging to Glu153 and H atom of OH group belonging to glucose. Because, the N-H group of Lys195 interacts with the O atom of latter OH group, reaction of Lys195 is more desirable than that of Lys199. In fact, glucose is placed in the vicinity of Lys195 along with electrostatic interaction and H-bonding to Lys195 and Lys199 as well as H-bonding with Glu153, which subsequently reacts with Lys195. Thus, Lys195 is the primary site in reaction of glucose with HSA.
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Affiliation(s)
- Rasoul Nasiri
- Department of Chemistry, Faculty of Sciences, Shahid Beheshti University, Evin, 19839-63113, Tehran, Iran
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46
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Tao Y, Rao ZH, Liu SQ. Insight derived from molecular dynamics simulation into substrate-induced changes in protein motions of proteinase K. J Biomol Struct Dyn 2010; 28:143-58. [PMID: 20645649 DOI: 10.1080/073911010010524953] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Because of the significant industrial, agricultural and biotechnological importance of serine protease proteinase K, it has been extensively investigated using experimental approaches such as X-ray crystallography, site-directed mutagenesis and kinetic measurement. However, detailed aspects of enzymatic mechanism such as substrate binding, release and relevant regulation remain unstudied. Molecular dynamics (MD) simulations of the proteinase K alone and in complex with the peptide substrate AAPA were performed to investigate the effect of substrate binding on the dynamics/molecular motions of proteinase K. The results indicate that during simulations the substrate-complexed proteinase K adopt a more compact and stable conformation than the substrate-free form. Further essential dynamics (ED) analysis reveals that the major internal motions are confined within a subspace of very small dimension. Upon substrate binding, the overall flexibility of the protease is reduced; and the noticeable displacements are observed not only in substrate-binding regions but also in regions opposite the substrate-binding groove/pockets. The dynamic pockets caused by the large concerted motions are proposed to be linked to the substrate recognition, binding, orientation and product release; and the significant displacements in regions opposite the binding groove/pockets are considered to play a role in modulating the dynamics of enzyme-substrate interaction. Our simulation results complement the biochemical and structural studies, highlighting the dynamic mechanism of the functional properties of proteinase K.
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Affiliation(s)
- Yan Tao
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming 650091, Yunnan, P R China
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47
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Varughese JF, Chalovich JM, Li Y. Molecular dynamics studies on troponin (TnI-TnT-TnC) complexes: insight into the regulation of muscle contraction. J Biomol Struct Dyn 2010; 28:159-74. [PMID: 20645650 DOI: 10.1080/07391102.2010.10507350] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Mutations of any subunit of the troponin complex may lead to serious disorders. Rational approaches to managing these disorders require knowledge of the complex interactions among the three subunits that are required for proper function. Molecular dynamics (MD) simulations were performed for both skeletal (sTn) and cardiac (cTn) troponin. The interactions and correlated motions among the three components of the troponin complex were analyzed using both Molecular Mechanics-Generalized Born Surface Area (MMGBSA) and cross-correlation techniques. The TnTH2 helix was strongly positively correlated with the two long helices of TnI. The C domain of TnC was positively correlated with TnI and TnT. The N domain of TnC was negatively correlated with TnI and TnT in cTn, but not in sTn. The two C-domain calcium-binding sites of TnC were dynamically correlated. The two regulatory N-domain calcium-binding sites of TnC were dynamically correlated, even though the calcium-binding site I is dysfunctional. The strong interaction residue pairs and the strong dynamically correlated residues pairs among the three components of troponin complexes were identified. These correlated motions are consistent with the idea that there is a high degree of cooperativity among the components of the regulatory complex in response to Ca(2+) and other effectors. This approach may give insight into the mechanism by which mutations of troponin cause disease. It is interesting that some observed disease causing mutations fall within regions of troponin that are strongly correlated or interacted.
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Affiliation(s)
- Jayson F Varughese
- Department of Chemistry, Brody School of Medicine, East Carolina University, Greenville, NC 27858, USA
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48
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Kahlon AK, Roy S, Sharma A. Molecular Docking Studies to Map the Binding Site of Squalene Synthase Inhibitors on Dehydrosqualene Synthase ofStaphylococcus Aureus. J Biomol Struct Dyn 2010; 28:201-10. [DOI: 10.1080/07391102.2010.10507353] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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49
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Shen HB, Chou KC. Virus-mPLoc: A Fusion Classifier for Viral Protein Subcellular Location Prediction by Incorporating Multiple Sites. J Biomol Struct Dyn 2010; 28:175-86. [PMID: 20645651 DOI: 10.1080/07391102.2010.10507351] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Mangels C, Kellner R, Einsiedel J, Weiglmeier PR, Rosch P, Gmeiner P, Schwarzinger S. The therapeutically anti-prion active antibody-fragment scFv-W226: paramagnetic relaxation-enhanced NMR spectroscopy aided structure elucidation of the paratope-epitope interface. J Biomol Struct Dyn 2010; 28:13-22. [PMID: 20476792 DOI: 10.1080/07391102.2010.10507340] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Antibodies have become indispensable reagents with numerous applications in biological and biotechnical analysis, in diagnostics as well as in therapy. In all cases, selective interaction with an epitope is crucial and depends on the conformation of the paratope. While epitopes are routinely mapped at high throughput, methods revealing structural insights on a rather short timescale are rare. We here demonstrate paramagnetic relaxation-enhanced (PRE) NMR spectroscopy to be a powerful tool unraveling structural information about epitope-orientation in a groove spanned by the complementary determining regions. In particular, we utilize the spin label TOAC, which is fused to the peptidic epitope using standard solid-phase chemistry and which is characterized by a reduced mobility compared to, e.g., spin labels attached to the side-chain functionalities of cysteine or lysine residues. We apply the method to determine the orientation of helix 1 of the prion protein, which is the epitope for the therapeutically anti-prion active scF(v) fragment W226.
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Affiliation(s)
- Christian Mangels
- Department of Biopolymers, Universitat Bayreuth, Universitatsstrasse 30, 95440 Bayreuth, Germany
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