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Molecular BioSystems

Timothy R Rudd, Mark D Preston, Edwin A Yates
In multicellular organisms, a large number of proteins interact with the polyanionic polysaccharides heparan sulphate (HS) and heparin. These interactions are usually assumed to be dominated by charge-charge interactions between the anionic carboxylate and/or sulfate groups of the polysaccharide and cationic amino acids of the protein. A major question is whether there exist conserved amino acid sequences for HS/heparin binding among these diverse proteins. Potentially conserved HS/heparin binding sequences were sought amongst 437 HS/heparin binding proteins...
March 20, 2017: Molecular BioSystems
Prachi Mehrotra, Gayatri Ramakrishnan, Gunasekaran Dhandapani, Narayanaswamy Srinivasan, Madathiparambil G Madanan
Leptospirosis, a potentially life-threatening disease, remains the most widespread zoonosis caused by pathogenic species of Leptospira. The pathogenic spirochaete, Leptospira interrogans, is characterized by its ability to permeate human host tissues rapidly and colonize multiple organs in the host. In spite of the efforts taken to comprehend the pathophysiology of the pathogen and the heterogeneity posed by L. interrogans, the current knowledge on the mechanism of pathogenesis is modest. In an attempt to contribute towards the same, we demonstrate the use of an established structure-based protocol coupled with information on subcellular localization of proteins and their tissue-specificity, in recognizing a set of 49 biologically feasible interactions potentially mediated by proteins of L...
March 15, 2017: Molecular BioSystems
L Michel Espinoza-Fonseca
Ca(2+) transport across the sarco/endoplasmic reticulum (SR) plays an essential role in intracellular Ca(2+) homeostasis, signalling, cell differentiation and muscle contractility. During SR Ca(2+) uptake and release, proton fluxes are required to balance the charge deficit generated by the exchange of Ca(2+) and other ions across the SR. During Ca(2+) uptake by the SR Ca(2+)-ATPase (SERCA), two protons are countertransported from the SR lumen to the cytosol, thus partially compensating for the charge moved by Ca(2+) transport...
March 14, 2017: Molecular BioSystems
R G Brajesh, Nikhil Raj, Supreet Saini
How does a transcription network arrive at the particular values of biochemical interactions defining it? These interactions define DNA-transcription factor interaction, degradation rates of proteins, promoter strengths, and communication of the environmental signal with the network. What is the structure of the fitness landscape that is defined by the space that these parameters can take on? To answer these questions, we simulate the simplest regulatory network: a transcription factor, R, and a target protein, T...
March 8, 2017: Molecular BioSystems
E D Spyrelli, A V Kyriazou, C Virgiliou, A Nakas, O Deda, V P Papageorgiou, A N Assimopoulou, H G Gika
Shikonin and its enantiomer alkannin, which are natural products, have been extensively studied in vitro and in vivo for, among others, their antitumor activity. The investigation of the molecular pathways involved in their action is of interest, since they are not yet clearly defined. Metabolic profiling in cells can provide a picture of a cell's phenotype upon intervention, assisting in the elucidation of the mechanism of action. In this study, the cytotoxic effect of shikonin on a human hepatocarcinoma cell line was studied...
March 7, 2017: Molecular BioSystems
Min Hyeon Shin, Hyun-Suk Lim
Protein folding is crucial for most proteins to achieve their correct three-dimensional conformations and function properly. Defects in protein folding frequently caused by mutations lead to a range of protein misfolding diseases, including Alzheimer's disease, Parkinson's disease, cystic fibrosis, amyloidosis, Gaucher disease, etc. One approach to treat these devastating diseases would be to use pharmacological chaperones, which are small-molecules that bind to and stabilize misfolded proteins, thereby correcting their pathogenic misfolding and rescuing their functions...
March 7, 2017: Molecular BioSystems
Cynthia Rangel-Chavez, Edgardo Galan-Vasquez, Agustino Martinez-Antonio
Genetic information in genomes is ordered, arranged in such a way that it constitutes a code, the so-called cis regulatory code. The regulatory machinery of the cell, termed trans-factors, decodes and expresses this information. In this way, genomes maintain a potential repertoire of genetic programs, parts of which are executed depending on the presence of active regulators in each condition. These genetic programs, executed by the regulatory machinery, have functional units in the genome delimited by punctuation-like marks...
March 3, 2017: Molecular BioSystems
Venkatesh Vaidyanathan, Vijay Naidu, Chi Hsiu-Juei Kao, Nishi Karunasinghe, Karen S Bishop, Alice Wang, Radha Pallati, Phillip Shepherd, Jonathan Masters, Shuotun Zhu, Megan Goudie, Mohanraj Krishnan, Anower Jabed, Gareth Marlow, Ajit Narayanan, Lynnette R Ferguson
Prostate cancer is one of the most significant health concerns for men worldwide. Numerous researchers carrying out molecular diagnostics have indicated that genetic interactions with biological and behavioral factors play an important role in the overall risk and prognosis of this disease. Single nucleotide polymorphisms (SNPs) are increasingly becoming strong biomarker candidates to identify susceptibility to prostate cancer. We carried out a gene × environment interaction analysis linked to aggressive and non-aggressive prostate cancer (PCa) with a number of SNPs...
March 2, 2017: Molecular BioSystems
Md Al Mehedi Hasan, Shamim Ahmad, Md Khademul Islam Molla
Predicting the subcellular locations of proteins can provide useful hints that reveal their functions, increase our understanding of the mechanisms of some diseases, and finally aid in the development of novel drugs. As the number of newly discovered proteins has been growing exponentially, which in turns, makes the subcellular localization prediction by purely laboratory tests prohibitively laborious and expensive. In this context, to tackle the challenges, computational methods are being developed as an alternative choice to aid biologists in selecting target proteins and designing related experiments...
March 1, 2017: Molecular BioSystems
Suchana Chakravarty, Debashis Barik
Various cellular decision making processes are regulated by bistable switches that take graded input signals and convert them to binary all-or-none responses. Traditionally, a bistable switch generated by a positive feedback loop is characterized either by a hysteretic signal response curve with two distinct signaling thresholds or by characterizing the bimodality of the response distribution in the bistable region. To identify the intrinsic bistability of a feedback regulated network, here we propose that bistability can be determined by correlating higher order moments and cumulants (≥2) of the joint steady state distributions of two components connected in a positive feedback loop...
March 1, 2017: Molecular BioSystems
Wenying He, Cangzhi Jia
Enhancers are cis-acting elements that play major roles in upregulating eukaryotic gene expression by providing binding sites for transcription factors and their complexes. Because enhancers are highly cell/tissue specific, lack common motifs, and are far from the target gene, the systematic and precise identification of enhancer regions in DNA sequences is a big challenge. In this study, we developed an enhancer prediction method called EnhancerPred2.0 by combining position-specific trinucleotide propensity (PSTNP) information with the electron-ion interaction potential (EIIP) values for trinucleotides, to predict enhancers and their subgroups...
February 27, 2017: Molecular BioSystems
Anil K Gorle, Amy L Bottomley, Elizabeth J Harry, J Grant Collins, F Richard Keene, Clifford E Woodward
Condensation studies of chromosomal DNA in E. coli with a tetranuclear ruthenium complex are carried out and images obtained with wide-field fluorescence microscopy. Remarkably different condensate morphologies resulted, depending upon the treatment protocol. The occurrence of condensed nucleoid spirals in live bacteria provides evidence for the transertion hypothesis.
February 24, 2017: Molecular BioSystems
Purva Bhatter, Karthik Raman, Vani Janakiraman
Microbial volatile organic compounds (VOCs) have gained prominence in the recent past for their potential use as disease markers. The discovery of microbial VOCs has benefited 'difficult to detect' diseases such as tuberculosis (TB). Few of the identified VOCs of Mycobacterium tuberculosis (Mtb) are currently being explored for their diagnostic potential. However, very little is known about the biosynthesis of these small lipophilic molecules. Here, we propose putative biosynthetic pathways in Mycobacterium tuberculosis for three VOCs, namely methyl nicotinate, methyl phenylacetate and methyl p-anisate, using computational approaches...
February 22, 2017: Molecular BioSystems
Mingxiao Zhao, Kim Kt Lau, Xian Zhou, Jianfang Wu, Jun Yang, Chang Wang
After a large-scale radiological accident, early-response biomarkers to assess radiation exposure over a broad dose range are not only the basis of rapid radiation triage, but are also the key to the rational use of limited medical resources and to the improvement of treatment efficiency. Because of its high throughput, rapid assays and minimally invasive sample collection, metabolomics has been applied to research into radiation exposure biomarkers in recent years. Due to the complexity of radiobiological effects, most of the potential biomarkers are both dose-dependent and time-dependent...
February 22, 2017: Molecular BioSystems
Huiming Cao, Yuzhen Sun, Ling Wang, Chunyan Zhao, Jianjie Fu, Aiqian Zhang
Polybrominated diphenyl ethers (PBDEs), one typical type of persistent environmental contaminant, have toxicological effects such as disrupting thyroid homeostasis in the human body. The high binding affinities of hydroxylated metabolites of PBDEs (OH-PBDEs) with transthyretin (TTR) were considered to be one major reason for their extraordinary capacity of passing through the blood-brain barrier via competitive thyroid hormone (T4) transport protein binding. Recent findings showed that sulfated PBDEs can be formed in human liver cytosol as phase-II metabolites...
February 20, 2017: Molecular BioSystems
Katelyn R Ludwig, Amanda B Hummon
Sepsis is a serious medical condition that occurs in 30% of patients in intensive care units (ICUs). Early detection of sepsis is key to prevent its progression to severe sepsis and septic shock, which can cause organ failure and death. Diagnostic criteria for sepsis are nonspecific and hinder a timely diagnosis in patients. Therefore, there is currently a large effort to detect biomarkers that can aid physicians in the diagnosis and prognosis of sepsis. Mass spectrometry is often the method of choice to detect metabolomic and proteomic changes that occur during sepsis progression...
February 16, 2017: Molecular BioSystems
Sadegh Sulaimany, Mohammad Khansari, Peyman Zarrineh, Madelaine Daianu, Neda Jahanshad, Paul M Thompson, Ali Masoudi-Nejad
Link prediction is a promising research area for modeling various types of networks and has mainly focused on predicting missing links. Link prediction methods may be valuable for describing brain connectivity, as it changes in Alzheimer's disease (AD) and its precursor, mild cognitive impairment (MCI). Here, we analyzed 3-tesla whole-brain diffusion-weighted images from 202 participants in the Alzheimer's Disease Neuroimaging Initiative (ADNI) - 50 healthy controls, 72 with earlyMCI (eMCI) and 38 with lateMCI (lMCI) and 42 AD patients...
February 15, 2017: Molecular BioSystems
Chang Peng, Xiaomei Luo, Shuo Li, Huichao Sun
Cardiac hypertrophy is a complex process involving highly coordinated but tight regulation of multiple elements, such as in epigenetics, which make an important contribution to myocardium remodeling and cardiac hypertrophy. Epigenetic regulations, particularly histone acetylation, have been implicated in cardiac hypertrophy, however, the exact mechanism is still largely unknown. In the present study, we explored the potential attenuating effects of Chinese herbal extract anacardic acid on phenylephrine-induced cardiac hypertrophy and the underlying mechanism...
February 14, 2017: Molecular BioSystems
Navid Nezafat, Mahboobeh Eslami, Manica Negahdaripour, Mohammad Reza Rahbar, Younes Ghasemi
Helicobacter pylori is the cunning bacterium that can live in the stomachs of many people without any symptoms, but gradually can lead to gastric cancer. Due to various obstacles, which are related to anti-H. pylori antibiotic therapy, recently developing an anti-H. pylori vaccine has attracted more attention. In this study, different immunoinformatics and computational vaccinology approaches were employed to design an efficient multi-epitope oral vaccine against H. pylori. Our multi-epitope vaccine is composed of heat labile enterotoxin IIc B (LT-IIc) that is used as a mucosal adjuvant to enhance vaccine immunogenicity for oral immunization, cartilage oligomeric matrix protein (COMP) to increase vaccine stability in acidic pH of gut, one experimentally protective antigen, OipA, and two hypothetical protective antigens, HP0487 and HP0906, and "CTGKSC" peptide motif that target epithelial microfold cells (M cells) to enhance vaccine uptake from the gut barrier...
February 14, 2017: Molecular BioSystems
Huili Guo, Yadong Yang, Feiyan Xue, Hong Zhang, Tiran Huang, Wenbin Liu, Huan Liu, Fenqiang Zhang, Mingfeng Yang, Chunmei Liu, Heshu Lu, Yansheng Zhang, Lanqing Ma
In order to elucidate the effect of flexible linker length on the catalytic efficiency of fusion proteins, two short flexible peptide linkers of various lengths were fused between Arabidopsis thaliana 4-coumaroyl-CoA ligase (4CL) and Polygonum cuspidatum stilbene synthase (STS) to generate fusion proteins 4CL-(GSG)n-STS (n ≤ 5) and 4CL-(GGGGS)n-STS (n ≤ 4). The fusion proteins were expressed in both Escherichia coli and Saccharomyces cerevisiae, and their bioactivities were tested in vitro and in vivo using purified proteins and engineered strains, respectively...
February 9, 2017: Molecular BioSystems
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