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Computational and Structural Biotechnology Journal

Federica Cossu, Mario Milani, Eloise Mastrangelo, Daniele Lecis
Inhibitor of apoptosis (IAP) proteins are characterized by the presence of the conserved baculoviral IAP repeat (BIR) domain that is involved in protein-protein interactions. IAPs were initially thought to be mainly responsible for caspase inhibition, acting as negative regulators of apoptosis, but later works have shown that IAPs also control a plethora of other different cellular pathways. As X-linked IAP (XIAP), and other IAP, levels are often deregulated in cancer cells and have been shown to correlate with patients' prognosis, several approaches have been pursued to inhibit their activity in order to restore apoptosis...
2019: Computational and Structural Biotechnology Journal
Yongsheng Yu, Shuangdi Li, Kai Wang, Xiaoping Wan
Melanoma differentiation-associated gene 9 (MDA-9)/Syntenin is a multidomain PDZ protein and identified as a key oncogene in melanoma initially. This protein contains a unique tandem PDZ domain architecture (PDZ1 and PDZ2 spaced by a 4-amino acid linker), an N-terminal domain (NTD) that is structurally uncharacterized and a short C-terminal domain (CTD). The PDZ1 domain is regarded as the PDZ signaling domain while PDZ2 served as the PDZ superfamily domain. It has various cellular roles by regulating many of major signaling pathways in numerous cancertypes...
2019: Computational and Structural Biotechnology Journal
Liam Grenier, Pingzhao Hu
As knowledge of the genetics behind inflammatory bowel disease (IBD) has continually improved, there has been a demand for methods that can use this data in a clinically significant way. Genome-wide association analyses for IBD have identified 232 risk genetic loci for the disorder. While identification of these risk loci enriches our understanding of the underlying biology of the disorder, their identification does not serve a clinical purpose. A potential use of this genetic information is to look for potential IBD drugs that target these loci in a procedure known as drug repurposing...
2019: Computational and Structural Biotechnology Journal
Denisa Maderankova, Robin Jugas, Karel Sedlar, Martin Vitek, Helena Skutkova
Species delineation based on bacterial genomes is an essential part of the research of prokaryotes. In silico genome-to-genome comparison methods are computationally demanding, but much less tedious and error prone than the wet-lab methods. In this paper, we present a novel method for the delineation of bacterial genomes based on genomic signal processing. The proposed method uses numerical representations of whole bacterial genomes, phase signal and cumulated phase signal, from which four parameters are derived for each genome...
2019: Computational and Structural Biotechnology Journal
Chien-Hui Wen, Shun-Chieh Hsu, Shan-Hui Hsu, Shu-Wei Chang
Biodegradable hydrogels have become promising materials for many biological applications in the past years. Recently, novel waterborne biodegradable polyurethane (WDPU) nanoparticles have been synthesized by a green water-based process, and serve as fundamental building blocks to form materials with great biocompatibility, biodegradability, and mechanical properties. However, the molecular structures and mechanisms of the WDPU nanoparticles and the relationship between the chemical compositions of the polymer segments and the material properties of the biodegradable hydrogels at macro-scale are still not well understood...
2019: Computational and Structural Biotechnology Journal
Qing Liu, Andreas Herrmann, Qiang Huang
As human phosphodiesterase (PDE) proteins are attractive drug targets, a large number of selective PDE inhibitors have been developed. However, since the catalytic sites of PDE isoforms are conserved in sequence and structure, it remains unclear how these inhibitors discriminate PDE isoforms in a selective manner. Here we perform long-time scale molecular dynamics (MD) simulations to investigate the spontaneous association processes of a highly selective PDE2A inhibitor (BAY60-7550) with the catalytic pockets of six PDE isoforms...
2019: Computational and Structural Biotechnology Journal
Norman John Mapes, Christopher Rodriguez, Pradeep Chowriappa, Sumeet Dua
Free radicals that form from reactive species of nitrogen and oxygen can react dangerously with cellular components and are involved with the pathogenesis of diabetes, cancer, Parkinson's, and heart disease. Cysteine amino acids, due to their reactive nature, are prone to oxidation by these free radicals. Determining which cysteines oxidize within proteins is crucial to our understanding of these chronic diseases. Wet lab techniques, like differential alkylation, to determine which cysteines oxidize are often expensive and time-consuming...
2019: Computational and Structural Biotechnology Journal
Juntao Li, Hengwei Zhang, Hui Jiang, Xuhui Guo, Yinli Zhang, Dan Qi, Jitian Guan, Zhenzhen Liu, Erxi Wu, Suxia Luo
The diagnostic performance difference between digital breast tomosynthesis (DBT) and conventional full-field digital mammography (FFDM) for breast suspicious calcifications from various populations is unclear. The objective of this study is to determine whether DBT exhibits the diagnostic advantage for breast suspicious calcifications from various populations compared with FFDM. Three hundred and five patients were enrolled (of which seven patients with bilateral lesions) and 312 breasts images were retrospectively analyzed by three radiologists independently...
2019: Computational and Structural Biotechnology Journal
Hirokazu Yano, Masaki Shintani, Masaru Tomita, Haruo Suzuki, Taku Oshima
Plasmids are genetic parasites of microorganisms. The genomes of naturally occurring plasmids are expected to be polished via natural selection to achieve long-term persistence in the microbial cell population. However, plasmid genomes are extremely diverse, and the rules governing plasmid genomes are not fully understood. Therefore, computationally designing plasmid genomes optimized for model and nonmodel organisms remains challenging. Here, we summarize current knowledge of the plasmid genome organization and the factors that can affect plasmid persistence, with the aim of constructing synthetic plasmids for use in gram-negative bacteria...
2019: Computational and Structural Biotechnology Journal
Sadia Zafar, Megin E Nguyen, Ramaiah Muthyala, Ishrat Jabeen, Yuk Y Sham
Human γ-Aminobutyric acid transporter 1 ( h GAT1) is a Na+ /Cl- dependent co-transporter that plays a key role in the inhibitory neurotransmission of GABA in the brain. Due to the lack of structural data, the exact co-transport mechanism of GABA reuptake by h GAT1 remains unclear. To examine the roles of the co-transport ions and the nature of their interactions with GABA, homology modeling and molecular dynamics simulations of the h GAT1 in the open-to-out conformation were carried out. Our study focused on the sequential preloading of Na+ and Cl- ions, followed by GABA binding...
2019: Computational and Structural Biotechnology Journal
Lei Chen, XiaoYong Pan, Yu-Hang Zhang, Min Liu, Tao Huang, Yu-Dong Cai
A tissue-specific gene expression shapes the formation of tissues, while gene expression changes reflect the immune response of the human body to environmental stimulations or pressure, particularly in disease conditions, such as cancers. A few genes are commonly expressed across tissues or various cancers, while others are not. To investigate the functional differences between widely and rarely expressed genes, we defined the genes that were expressed in 32 normal tissues/cancers (i.e., called widely expressed genes; FPKM >1 in all samples) and those that were not detected (i...
2019: Computational and Structural Biotechnology Journal
Bing Niu, Yi Lu, Jianying Wang, Yan Hu, Jiahui Chen, Qin Chen, Guangwu He, Linfeng Zheng
Avian influenza is a serious zoonotic infectious disease with huge negative impacts on local poultry farming, human health and social stability. Therefore, the design of new compounds against avian influenza has been the focus in this field. In this study, computational methods were applied to investigate the compounds with neuraminidase inhibitory activity. First, 2D-SAR model was built to recognize neuraminidase inhibitors (NAIs). As a result, the accuracy of 10 cross-validation and independent tests is 96...
2019: Computational and Structural Biotechnology Journal
Brandall L Ingle, Bisesh Shrestha, Margarita C De Jesus, Heather M Conrad-Webb, Mary E Anderson, Thomas R Cundari
The second step in the biosynthesis of the cellular antioxidant glutathione (GSH) is catalyzed by human glutathione synthetase (hGS), a negatively cooperative homodimer. Patients with mutations in hGS have been reported to exhibit a range of symptoms from hemolytic anemia and metabolic acidosis to neurological disorders and premature death. Several patient mutations occur in the S-loop of hGS, a series of residues near the negatively cooperative γ-GC substrate binding site. Experimental point mutations and molecular dynamic simulations show the S-loop not only binds γ-GC through a salt bridge and multiple hydrogen bonds, but the residues also modulate allosteric communication in hGS...
2019: Computational and Structural Biotechnology Journal
Xuanhao Zhao, Li Li, Gengnan Yu, Shuangyan Zhang, Yumei Li, Qiong Wu, Xiaoting Huang, Wenjie Mei
Polypyridine Ru(II) complexes have long been deemed to excellent antitumor agents that inhibit the proliferation of breast cancer cells. Nevertheless, their effects on the metastatic potency of breast cancer cells need further research. Herein, a class of polypyridine Ru(II) complexes coordinated with phenazine derivates (DPPZ) ([Ru(bpy)2 (DPPZ-R)](ClO4 )2 , Ru(bpy) 2 DPPZ : R = -H, Ru(bpy) 2 BrDPPZ : R = -Br, Ru(bpy) 2 MDPPZ : R = -CH3 , Ru(bpy)2BnDPPZ : R = -acene, Ru(bpy) 2 BEDPPZ : R = -C ≡ C(C6 H5 )) was synthesized by introducing different substituent groups to regulate the electron cloud density and planarity of the main ligands...
2019: Computational and Structural Biotechnology Journal
Kristen Kalbfleisch, Sasmit Deshmukh, Carmen Mei, Moriam Ore, Wayne Williams, Ibrahim Durowoju, Jessica Duprez, Sylvie Morin, Bruce Carpick, Marina Kirkitadze
Purpose: The goal of this study is to set an empirical baseline to map the structure-function relation of the antigens from the commercialized vaccine products. Methods: To study the structural changes of protein antigens after adsorption several analytical tools including DLS, FTIR, Fluorescence, LD, and SEM have been used. Results: All antigens have shown wide range of hydrodynamic diameter from 7 nm to 182 nm. Upon adjuvantation, the size distribution has become narrow, ranging from 10 to 12 μm, and has been driven by the derived diameter of aluminum phosphate (AlPO4 ) adjuvant...
2019: Computational and Structural Biotechnology Journal
Nomathamsanqa Resegofetse Maimela, Shasha Liu, Yi Zhang
Studies have reported a positive correlation between elevated CD8+ T cells in the tumor microenvironment (TME) and good prognosis in cancer. However, the mechanisms linking T cell tumor-infiltration and tumor rejection are yet to be fully understood. The cells and factors of the TME facilitate tumor development in various ways. CD8+ T cell function is influenced by a number of factors, including CD8+ T cell trafficking and localization into tumor sites; as well as CD8+ T cell growth and differentiation. This review highlights recent literature as well as currently evolving concepts regarding the fates of CD8+ T cells in the TME from three different aspects CD8+ T cell trafficking, differentiation and function...
2019: Computational and Structural Biotechnology Journal
Wipawadee Suwannapan, Pramote Chumnanpuen, Teerasak E-Kobon
This study aimed to investigate the conserved FAD-binding region of the L-amino acid oxidase ( LAAO ) genes in twelve gastropod genera commonly found in Thailand compared to those in other organisms using molecular cloning, nucleotide sequencing and bioinformatics analysis. Genomic DNA of gastropods and other invertebrates was extracted and screened using primers specific to the conserved FAD-binding region of LAAO . The amplified 143-bp fragments were cloned and sequenced. The obtained nucleotide sequences of 21 samples were aligned and phylogenetically compared to the LAAO -conserved FAD-binding regions of 210 other organisms from the NCBI database...
2018: Computational and Structural Biotechnology Journal
Baiqing Li, Chunfeng Ma, Xiaoyong Zhao, Zhigang Hu, Tengfei Du, Xuanming Xu, Zhonghua Wang, Jianping Lin
Traditional Chinese Medicine (TCM) has a long history of widespread clinical applications, especially in East Asia, and is becoming frequently used in Western countries. However, owing to extreme complicacy in both chemical ingredients and mechanism of action, a deep understanding of TCM is still difficult. To accelerate the modernization and popularization of TCM, a single comprehensive database is required, containing a wealth of TCM-related information and equipped with complete analytical tools. Here we present YaTCM (Yet another Traditional Chinese Medicine database), a free web-based toolkit, which provides comprehensive TCM information and is furnished with analysis tools...
2018: Computational and Structural Biotechnology Journal
Maytham Hussein, Mei-Ling Han, Yan Zhu, Elena K Schneider-Futschik, Xiaohan Hu, Qi Tony Zhou, Yu-Wei Lin, Dovile Anderson, Darren J Creek, Daniel Hoyer, Jian Li, Tony Velkov
Polymyxins are amongst the most important antibiotics in modern medicine, in recent times their clinical utility has been overshadowed by nosocomial outbreaks of polymyxin resistant MDR Gram-negative 'superbugs'. An effective strategy to surmount polymyxin resistance is combination therapy with FDA-approved non-antibiotic drugs. Herein we used untargeted metabolomics to investigate the mechanism(s) of synergy between polymyxin B and the selective estrogen receptor modulator (SERM) tamoxifen against a polymyxin-resistant MDR cystic fibrosis (CF) Pseudomonas aeruginosa FADDI-PA006 isolate (polymyxin B MIC=8 mg/L , it is an MDR polymyxin resistant P...
2018: Computational and Structural Biotechnology Journal
Fisayo A Olotu, Geraldene Munsamy, Mahmoud E S Soliman
Over the years, numerous synthetic approaches have been utilized in drug design to improve the pharmacological properties of naturally derived compounds and most importantly, minimize toxic effects associated with their transition to drugs. The reduction of complex bioderived compounds to simpler bioactive fragments has been identified as a viable strategy to develop lead compounds with improved activities and minimal toxicities. Although this 'reductive' strategy has been widely exemplified, underlying biological events remain unresolved, hence the unanswered question remains how does the fragmentation of a natural compound improve its bioactivity and reduce toxicities? Herein, using a combinatorial approach, we initialize a computational "proof-of- concept" to expound the differential pharmacological and antagonistic activities of a natural compound, Anguinomycin D, and its synthetic fragment, SB640 towards Exportin Chromosome Region Maintenance 1 (CRM1)...
2018: Computational and Structural Biotechnology Journal
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