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Molecular BioSystems

Yu Wu, Yonghong Li, Yanjuan Jia, Chaojun Wei, Hui Xu, Rui Guo, Yuanting Li, Jing Jia, Xiaoming Qi, Xiaoling Gao
Hypothalamic dysfunction is a key factor in depression; increasing evidence highlights neuroinflammation abnormalities as well as imbalances in neurotransmitters and the purinergic system in the pathophysiology of depression. However, little is known about the metabolomic changes in the hypothalamus of depressed patients with neuroinflammation. Herein, taking advantage of the well-established lipopolysaccharide (LPS)-induced depression mouse model, we measured metabolic changes in the hypothalamus using gas chromatography-mass spectrometry (GC-MS)...
November 21, 2017: Molecular BioSystems
M Tomin, S Tomić
Correction for 'Dynamic properties of dipeptidyl peptidase III from Bacteroides thetaiotaomicron and the structural basis for its substrate specificity - a computational study' by M. Tomin et al., Mol. BioSyst., 2017, 13, 2407-2417.
November 21, 2017: Molecular BioSystems
Harshavardhan Khare, Debayan Dey, Chilakapati Madhu, Dillip Senapati, Srinivasarao Raghothama, Thimmaiah Govindaraju, Suryanarayanarao Ramakumar
A cationic terminal extension or tail is a common feature of many DNA-binding proteins. We show that a particular type of tail rich in proline, alanine and lysine belongs to the class of 'flexible disorder' and consists of characteristic pentapeptide repeats. Our designed peptides, (AAKKA)1-4 and (PAKKA)1-4 , represent the tails of several bacterial DNA-binding proteins. Enhanced conformational sampling of these representative peptides using accelerated molecular dynamic simulations supported by circular dichroism spectroscopy and nuclear magnetic resonance studies demonstrates the role of frequent and interspersed prolines in augmenting conformational heterogeneity of the peptide backbone...
November 21, 2017: Molecular BioSystems
Goutam Mukherjee, Arumay Pal, Yaakov Levy
In prokaryotes, the RecA protein catalyzes the repair and strand exchange of double-stranded DNA. RecA binds to single-stranded DNA (ssDNA) and forms a presynaptic complex in which the protein polymerizes around the ssDNA to form a right-handed helical nucleoprotein filament structure. In the present work, the mechanism for the formation of the RecA-ssDNA filament structure is modeled using coarse-grained molecular dynamics simulations. Information from the X-ray structure was used to model the protein itself but not its interactions; the interactions between the protein and the ssDNA were modeled solely by electrostatic, aromatic, and repulsive energies...
November 21, 2017: Molecular BioSystems
Hansol Im, Sujin Lee, Steven A Soper, Robert J Mitchell
The prevalence of Staphylococcus aureus worldwide as a nosocomial infectious agent is recognized but the reason behind the spread of this bacterium has remained elusive. Here, we hypothesized that the communication of S. aureus might benefit from it blocking other bacteria from establishing themselves on the surface. This was found to be the case for several pathogens as the S. aureus supernatant curtailed their ability to form biofilms. Subsequent analyses using Acinetobacter baumannii as a model found this effect is primarily mediated by S...
November 21, 2017: Molecular BioSystems
Lakshmi Prabhu, Lan Chen, Han Wei, Özlem Demir, Ahmad Safa, Lifan Zeng, Rommie E Amaro, Bert H O'Neil, Zhon-Yin Zhang, Tao Lu
The protein arginine methyltransferase (PRMT) family of enzymes comprises nine family members in mammals. They catalyze arginine methylation, either monomethylation or symmetric/asymmetric dimethylation of histone and non-histone proteins. PRMT methylation of its substrate proteins modulates cellular processes such as signal transduction, transcription, and mRNA splicing. Recent studies have linked overexpression of PRMT5, a member of the PRMT superfamily, to oncogenesis, making it a potential target for cancer therapy...
November 21, 2017: Molecular BioSystems
Xue Yan Yam, Peter R Preiser
Host immune evasion is a key strategy for the continual survival of many microbial pathogens including Apicomplexan protozoan: Plasmodium spp., the causative agent of Malaria. The malaria parasite has evolved a variety of mechanisms to evade the host immune responses within its two hosts: the female Anopheles mosquito vector and vertebrate host. In this review, we will focus on the molecular mechanisms of the immune evasion strategies used by the Plasmodium parasite at the blood stage which is responsible for the clinical manifestations of human malaria...
November 21, 2017: Molecular BioSystems
Jutty Rajan Prashanth, Sebastien Dutertre, Richard James Lewis
Cone snails are predatory gastropods whose neurotoxic venom peptides (conotoxins) have been extensively studied for pharmacological probes, venom evolution mechanisms and potential therapeutics. Conotoxins have a wide range of structural and functional classes that continue to undergo accelerated evolution that underlies the rapid expansion of the genus over their short evolutionary history. A number of pharmacological classes, driven by separately evolved defensive and predatory venoms, have been hypothesised to facilitate shifts in prey that exemplify the adaptability of cone snails...
November 21, 2017: Molecular BioSystems
Arumugam Kamaladevi, Shanmugam Marudhupandiyan, Krishnaswamy Balamurugan
Infectious diseases caused by bacterial pathogens pose a major concern to public health and, thus, greater attention must be given to providing insightful knowledge on host-pathogen interactions. There are several theories addressing the dynamics of complex mechanisms of host-pathogen interactions. The availability of an ample number of universally accepted model systems, including vertebrates, invertebrates, and mammalian cells, provides in-depth transcriptomics data to evaluate these complex mechanisms during host-pathogen interactions...
November 21, 2017: Molecular BioSystems
Andrea Polo, Chiara Nittoli, Anna Crispo, Teresa Langastro, Stefania Cocco, Lorella Severino, Michelino De Laurentiis, Gennaro Ciliberto, Maurizio Montella, Alfredo Budillon, Susan Costantini
Endocrine disrupting chemicals (EDCs) are natural or synthetic exogenous substances affecting human health. Although present at low concentrations in the environment, they can cause a broad range of negative effects on the endocrine functions by mimicking the action of steroid hormones due to their structural similarity. Hormonal unbalance can play an important role in carcinogenesis at any stage of disease. In the case of the breast cancer, EDCs directly affect the transformation of normal breast cells into cancer cells by interfering with hormonal regulation and by inducing the alteration of factors that regulate gene expression...
November 21, 2017: Molecular BioSystems
Paola Lecca, Fabio Bagagiolo, Marina Scarpa
In a biological cell, cellular functions and the genetic regulatory apparatus are implemented and controlled by complex networks of chemical reactions involving genes, proteins, and enzymes. Accurate computational models are indispensable means for understanding the mechanisms behind the evolution of a complex system, not always explored with wet lab experiments. To serve their purpose, computational models, however, should be able to describe and simulate the complexity of a biological system in many of its aspects...
November 21, 2017: Molecular BioSystems
Kelly R Karch, Marie-France Langelier, John M Pascal, Benjamin A Garcia
ADP-ribosylation is a protein post-translational modification catalyzed by ADP-ribose transferases (ARTs). ART activity is critical in mediating many cellular processes, and is required for DNA damage repair. All five histone proteins are extensively ADP-ribosylated by ARTs upon induction of DNA damage. However, how these modifications aid in repair processes is largely unknown, primarily due to lack of knowledge about where they site-specifically occur on histones. Here, we conduct a comprehensive analysis of histone Asp/Glu ADP-ribosylation sites upon DNA damage induced by dimethyl sulfate (DMS)...
November 21, 2017: Molecular BioSystems
Lihong Peng, Yeqing Chen, Ning Ma, Xing Chen
An increasing amount of evidence indicates that microRNAs (miRNAs) are closely related to many important biological processes and play a significant role in various human diseases. More and more researchers have begun to seek effective methods to predict potential miRNA-disease associations. However, reliable computational methods to predict potential disease-related miRNAs are lacking. In this study, we developed a new miRNA-disease association prediction model called Negative-Aware and rating-based Recommendation algorithm for miRNA-Disease Association prediction (NARRMDA) based on the known miRNA-disease associations in the HMDD database, miRNA functional similarity, disease semantic similarity and Gaussian interaction profile kernel similarity...
November 21, 2017: Molecular BioSystems
Arup Panda, Debarun Acharya, Tapash Chandra Ghosh
Expression level provides important clues about gene function. Previously, various efforts have been undertaken to profile human genes according to their expression level. Intrinsically disordered proteins (IDPs) do not adopt any rigid conformation under physiological conditions, however, are considered as an important functional class in all domains of life. Based on a human tissue-averaged gene expression level, previous studies showed that IDPs are expressed at a lower level than ordered globular proteins...
November 21, 2017: Molecular BioSystems
Alexandra A Kuznetsova, Danila A Iakovlev, Inna V Misovets, Alexander A Ishchenko, Murat K Saparbaev, Nikita A Kuznetsov, Olga S Fedorova
In all organisms, DNA glycosylases initiate base excision repair pathways resulting in removal of aberrant bases from DNA. Human SMUG1 belongs to the superfamily of uracil-DNA glycosylases catalyzing the hydrolysis of the N-glycosidic bond of uridine and uridine lesions bearing oxidized groups at C5: 5-hydroxymethyluridine (5hmU), 5-formyluridine (5fU), and 5-hydroxyuridine (5hoU). An apurinic/apyrimidinic (AP) site formed as the product of an N-glycosylase reaction is tightly bound to hSMUG1, thus inhibiting the downstream action of AP-endonuclease APE1...
November 21, 2017: Molecular BioSystems
Maria Dermit, Martin Dodel, Faraz K Mardakheh
Regulation of protein translation constitutes a crucial step in control of gene expression. In comparison to transcriptional regulation, however, translational control has remained a significantly under-studied layer of gene expression. This trend is now beginning to shift thanks to recent advances in next-generation sequencing, proteomics, and microscopy based methodologies which allow accurate monitoring of protein translation rates, from single target messenger RNA molecules to genome-wide scale studies...
November 21, 2017: Molecular BioSystems
Cedrix J Dongmo Foumthuim, Alessandra Corazza, Gennaro Esposito, Federico Fogolari
Hydrophobic surfaces are known to adsorb and unfold proteins, a process that has been studied only for a few proteins. Here we address the interaction of β2-microglobulin, a paradigmatic protein for the study of amyloidogenesis, with hydrophobic surfaces. A system with 27 copies of the protein surrounded by a model cubic hydrophobic box is studied by implicit solvent molecular dynamics simulations. Most proteins adsorb on the walls of the box without major distortions in local geometry, whereas free molecules maintain proper structures and fluctuations as observed in explicit solvent molecular dynamics simulations...
November 21, 2017: Molecular BioSystems
Wandaliz Torres-García, Maribella Domenech
Hedgehog signaling (Hh) has been shown to be hyper-activated in several cancers. However, active Hh signaling can promote or inhibit tumor growth; thus identification of markers beyond main canonical Hh target genes is needed to improve patient selection and clinical outcome in response to Hh inhibitors. Cancer-associated fibroblasts (CAFs) have been linked with tumor progression and beneficial response to Hh inhibitors. Thus, we hypothesized that genes associated with Hh-activated CAFs can be used for stratification of tumors that will benefit from Hh inhibitors...
November 21, 2017: Molecular BioSystems
Swarnendu Banerjee, Abhishek Subramanian, Joydev Chattopadhyay, Ram Rup Sarkar
Toxic cyanobacteria blooms populate water bodies by consuming external nutrients and releasing cyanotoxins that are detrimental for other aquatic species, producing a significant impact on the plankton ecosystem and food web. To exercise population-level control of toxin production, understanding the biochemical mechanisms that explain cyanotoxin regulation within a bacterial cell is of utmost importance. In this study, we explore the mechanistic events to investigate the dependence of toxin microcystin on external nitrogen, a known regulator of the toxin, and for the first time, propose a kinetic model that analyzes the intracellular conditions required to ensure nitrogen dependence on microcystin...
November 21, 2017: Molecular BioSystems
Hafeez Ur Rehman, Inam Bari, Anwar Ali, Haroon Mahmood
Accurate elucidation of genome wide protein-protein interactions is crucial for understanding the regulatory processes of the cell. High-throughput techniques, such as the yeast-2-hybrid (Y2H) assay, co-immunoprecipitation (co-IP), mass spectrometric (MS) protein complex identification, affinity purification (AP) etc., are generally relied upon to determine protein interactions. Unfortunately, each type of method is inherently subject to different types of noise and results in false positive interactions. On the other hand, precise understanding of proteins, especially knowledge of their functional associations is necessary for understanding how complex molecular machines function...
November 21, 2017: Molecular BioSystems
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