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https://www.readbyqxmd.com/read/28335409/the-formyl-peptide-receptors-diversity-of-ligands-and-mechanism-for-recognition
#1
REVIEW
Hui-Qiong He, Richard D Ye
The formyl peptide receptors (FPRs) are G protein-coupled receptors that transduce chemotactic signals in phagocytes and mediate host-defense as well as inflammatory responses including cell adhesion, directed migration, granule release and superoxide production. In recent years, the cellular distribution and biological functions of FPRs have expanded to include additional roles in homeostasis of organ functions and modulation of inflammation. In a prototype, FPRs recognize peptides containing N-formylated methionine such as those produced in bacteria and mitochondria, thereby serving as pattern recognition receptors...
March 13, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28334755/tracking-fluctuation-hotspots-on-the-yeast-ribosome-through-the-elongation-cycle
#2
Suna P Gulay, Sujal Bista, Amitabh Varshney, Serdal Kirmizialtin, Karissa Y Sanbonmatsu, Jonathan D Dinman
Chemical modification was used to quantitatively determine the flexibility of nearly the entire rRNA component of the yeast ribosome through 8 discrete stages of translational elongation, revealing novel observations at the gross and fine-scales. These include (i) the bulk transfer of energy through the intersubunit bridges from the large to the small subunit after peptidyltransfer, (ii) differences in the interaction of the sarcin ricin loop with the two elongation factors and (iii) networked information exchange pathways that may functionally facilitate intra- and intersubunit coordination, including the 5...
February 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334215/systematic-inference-of-functional-phosphorylation-events-in-yeast-metabolism
#3
Yu Chen, Yonghong Wang, Jens Nielsen
Motivation: Protein phosphorylation is a post-translational modification that affects proteins by changing their structure and conformation in a rapid and reversible way, and it is an important mechanism for metabolic regulation in cells. Phosphoproteomics enables high-throughput identification of phosphorylation events on metabolic enzymes, but identifying functional phosphorylation events still requires more detailed biochemical characterization. Therefore, development of computational methods for investigating unknown functions of a large number of phosphorylation events identified by phosphoproteomics has received increased attention...
March 2, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334084/molecular-dynamics-recipes-for-genome-research
#4
Tommaso Biagini, Giovanni Chillemi, Gianluigi Mazzoccoli, Alessandro Grottesi, Caterina Fusilli, Daniele Capocefalo, Stefano Castellana, Angelo Luigi Vescovi, Tommaso Mazza
Molecular dynamics (MD) simulation allows one to predict the time evolution of a system of interacting particles. It is widely used in physics, chemistry and biology to address specific questions about the structural properties and dynamical mechanisms of model systems. MD earned a great success in genome research, as it proved to be beneficial in sorting pathogenic from neutral genomic mutations. Considering their computational requirements, simulations are commonly performed on HPC computing devices, which are generally expensive and hard to administer...
February 18, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28333338/drug-discovery-for-male-subfertility-using-high-throughput-screening-a-new-approach-to-an-unsolved-problem
#5
Sarah J Martins da Silva, Sean G Brown, Keith Sutton, Louise V King, Halil Ruso, David W Gray, Paul G Wyatt, Mark C Kelly, Christopher L R Barratt, Anthony G Hope
STUDY QUESTION: Can pharma drug discovery approaches be utilized to transform investigation into novel therapeutics for male infertility? SUMMARY ANSWER: High-throughput screening (HTS) is a viable approach to much-needed drug discovery for male factor infertility. WHAT IS KNOWN ALREADY: There is both huge demand and a genuine clinical need for new treatment options for infertile men. However, the time, effort and resources required for drug discovery are currently exorbitant, due to the unique challenges of the cellular, physical and functional properties of human spermatozoa and a lack of appropriate assay platform...
March 16, 2017: Human Reproduction
https://www.readbyqxmd.com/read/28332863/male-and-female-worldsid-and-post-mortem-human-subject-responses-in-full-scale-vehicle-tests
#6
Narayan Yoganandan, John Humm, Frank Pintar, Heather Rhule, Kevin Moorhouse, Brian Suntay, Jim Stricklin, Rodney Rudd, Matthew Craig
Structured ABSTRACT Objective: To compare the responses of male and female WorldSID dummies with post mortem human subject (PMHS) responses in full-scale vehicle tests. METHODS: Tests were conducted according to the FMVSS-214 protocols and using the United States Side impact New Car Assessment Program change in velocity to match PMHS experiments, published earlier. Moving deformable barrier (MDB) tests were conducted with the male and female surrogates in the left front and left rear seats...
March 23, 2017: Traffic Injury Prevention
https://www.readbyqxmd.com/read/28331186/disentangling-constraints-using-viability-evolution-principles-in-integrative-modeling-of-macromolecular-assemblies
#7
Giorgio Tamò, Andrea Maesani, Sylvain Träger, Matteo T Degiacomi, Dario Floreano, Matteo Dal Peraro
Predicting the structure of large molecular assemblies remains a challenging task in structural biology when using integrative modeling approaches. One of the main issues stems from the treatment of heterogeneous experimental data used to predict the architecture of native complexes. We propose a new method, applied here for the first time to a set of symmetrical complexes, based on evolutionary computation that treats every available experimental input independently, bypassing the need to balance weight components assigned to aggregated fitness functions during optimization...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28328543/challenges-in-describing-ribosome-dynamics
#8
Kien Nguyen, Paul Charles Whitford
For decades, protein folding and functional dynamics have been described in terms of diffusive motion across an underlying energy landscape. With continued advances in structural biology and high-performance computing, the field is positioned to extend these approaches to large biomolecular assemblies. Through the application of energy landscape techniques to the ribosome, one may work towards establishing a comprehensive description of the dynamics, which will bridge theoretical concepts and experimental observations...
March 22, 2017: Physical Biology
https://www.readbyqxmd.com/read/28327660/quantitative-volumetric-raman-imaging-of-three-dimensional-cell-cultures
#9
Charalambos Kallepitis, Mads S Bergholt, Manuel M Mazo, Vincent Leonardo, Stacey C Skaalure, Stephanie A Maynard, Molly M Stevens
The ability to simultaneously image multiple biomolecules in biologically relevant three-dimensional (3D) cell culture environments would contribute greatly to the understanding of complex cellular mechanisms and cell-material interactions. Here, we present a computational framework for label-free quantitative volumetric Raman imaging (qVRI). We apply qVRI to a selection of biological systems: human pluripotent stem cells with their cardiac derivatives, monocytes and monocyte-derived macrophages in conventional cell culture systems and mesenchymal stem cells inside biomimetic hydrogels that supplied a 3D cell culture environment...
March 22, 2017: Nature Communications
https://www.readbyqxmd.com/read/28327306/design-synthesis-antibacterial-activity-and-docking-study-of-some-new-trimethoprim-derivatives
#10
Umer Rashid, Waqas Ahmad, Syed Fahad Hassan, Naveeda Akhtar Qureshi, Basit Niaz, Bakhtiar Muhammad, Sameera Imdad, Muhammad Sajid
In present study, nineteen novel trimethoprim (TMP) derivatives were designed, synthesized and evaluated for their antibacterial potential. Hydroxy trimethoprim 2 (HTMP) was synthesized by following the demethylation of 4-methoxy group at trimethoxy benzyl ring of TMP. Structure-activity relationship (SAR) studies were explored on HTMP by incorporating various substituents leading to the identification of some new compounds with improved antibacterial activities. The results revealed that the introduction of benzyloxy (4a-e) and phenyl ethanone (5a-e) group at 4-position of dimethoxy benzyl ring leads to overall increase in the antibacterial activity...
December 1, 2016: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/28324757/perceptual-category-learning-and-visual-processing-an-exercise-in-computational-cognitive-neuroscience
#11
George Cantwell, Maximilian Riesenhuber, Jessica L Roeder, F Gregory Ashby
The field of computational cognitive neuroscience (CCN) builds and tests neurobiologically detailed computational models that account for both behavioral and neuroscience data. This article leverages a key advantage of CCN-namely, that it should be possible to interface different CCN models in a plug-and-play fashion-to produce a new and biologically detailed model of perceptual category learning. The new model was created from two existing CCN models: the HMAX model of visual object processing and the COVIS model of category learning...
March 6, 2017: Neural Networks: the Official Journal of the International Neural Network Society
https://www.readbyqxmd.com/read/28320968/numerosity-representation-is-encoded-in-human-subcortex
#12
Elliot Collins, Joonkoo Park, Marlene Behrmann
Certain numerical abilities appear to be relatively ubiquitous in the animal kingdom, including the ability to recognize and differentiate relative quantities. This skill is present in human adults and children, as well as in nonhuman primates and, perhaps surprisingly, is also demonstrated by lower species such as mosquitofish and spiders, despite the absence of cortical computation available to primates. This ubiquity of numerical competence suggests that representations that connect to numerical tasks are likely subserved by evolutionarily conserved regions of the nervous system...
March 20, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28320905/insights-into-the-deactivation-of-5-bromouracil-after-ultraviolet-excitation
#13
Francesca Peccati, Sebastian Mai, Leticia González
5-Bromouracil is a nucleobase analogue that can replace thymine in DNA strands and acts as a strong radiosensitizer, with potential applications in molecular biology and cancer therapy. Here, the deactivation of 5-bromouracil after ultraviolet irradiation is investigated in the singlet and triplet manifold by accurate quantum chemistry calculations and non-adiabatic dynamics simulations. It is found that, after irradiation to the bright ππ* state, three main relaxation pathways are, in principle, possible: relaxation back to the ground state, intersystem crossing (ISC) and C-Br photodissociation...
April 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/28319390/qualitative-behavior-of-the-low-frequency-vibrational-dynamics-of-microtubules-and-the-surrounding-water
#14
Jeremy M Moix, James E Parker, Ibtissam Echchgadda
The dynamics of the low-frequency vibrational modes of microtubules play a key role in many theoretical models regarding their biological function. We analyze these dynamics through large scale, classical molecular dynamics simulations of a microtubule composed of 42 tubulin heterodimers to provide insights into the qualitative nature of the vibrational energy absorption and dissipation mechanisms. The computed microtubule absorption spectra and vibrational density of states in the terahertz regime are presented, along with an analysis of the vibrational dephasing rates of the tubulin monomer center of mass dynamics, which are shown to be overdamped...
March 20, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28319238/behavioral-and-neural-constraints-on-hierarchical-representations
#15
Odelia Schwartz, Luis Gonzalo Sanchez Giraldo
Central to behavior and cognition is the way that sensory stimuli are represented in neural systems. The distributions over such stimuli enjoy rich structure; however, how the brain captures and exploits these regularities is unclear. Here, we consider different sources of perhaps the most prevalent form of structure, namely hierarchies, in one of its most prevalent cases, namely the representation of images. We review experimental approaches across a range of subfields, spanning inference, memory recall, and visual adaptation, to investigate how these constrain hierarchical representations...
March 1, 2017: Journal of Vision
https://www.readbyqxmd.com/read/28314103/computational-study-of-the-forces-driving-aggregation-of-ultrasmall-nanoparticles-in-biological-fluids
#16
Sergio A Hassan
Nanoparticle (NP) aggregation can lead to prolonged retention in tissues or embolism, among other adverse effects. Successful use in biomedicine thus requires the capability to make NPs with limited aggregative potential. Rational design is presently a challenge due to incomplete knowledge of their interactions in biofluids. Recently, ultrasmall gold NPs passivated with endogenous antioxidant glutathione have shown promise for use in vivo. Computer simulations are here conducted to identify the forces underlying aggregation (or lack thereof) of these NPs in a cell culture...
March 21, 2017: ACS Nano
https://www.readbyqxmd.com/read/28306551/master-equations-and-the-theory-of-stochastic-path-integrals
#17
Markus F Weber, Erwin Frey
This review provides a pedagogic and self-contained introduction to master equations and to their representation by path integrals. Since the 1930s, master equations have served as a fundamental tool to understand the role of fluctuations in complex biological, chemical, and physical systems. Despite their simple appearance, analyses of master equations most often rely on low-noise approximations such as the Kramers-Moyal or the system size expansion, or require ad-hoc closure schemes for the derivation of low-order moment equations...
April 2017: Reports on Progress in Physics
https://www.readbyqxmd.com/read/28303031/a-biologically-validated-hcv-e1e2-heterodimer-structural-model
#18
Matteo Castelli, Nicola Clementi, Jennifer Pfaff, Giuseppe A Sautto, Roberta A Diotti, Roberto Burioni, Benjamin J Doranz, Matteo Dal Peraro, Massimo Clementi, Nicasio Mancini
The design of vaccine strategies and the development of drugs targeting the early stages of Hepatitis C virus (HCV) infection are hampered by the lack of structural information about its surface glycoproteins E1 and E2, the two constituents of HCV entry machinery. Despite the recent crystal resolution of limited versions of both proteins in truncated form, a complete picture of the E1E2 complex is still missing. Here we combined deep computational analysis of E1E2 secondary, tertiary and quaternary structure with functional and immunological mutational analysis across E1E2 in order to propose an in silico model for the ectodomain of the E1E2 heterodimer...
March 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28302551/role-of-structural-bioinformatics-in-drug-discovery-by-computational-snp-analysis-a-proposed-protocol-for-analyzing-variation-at-the-protein-level
#19
REVIEW
David K Brown, Özlem Tastan Bishop
With the completion of the human genome project at the beginning of the 21st century, the biological sciences entered an unprecedented age of data generation, and made its first steps toward an era of personalized medicine. This abundance of sequence data has led to the proliferation of numerous sequence-based techniques for associating variation with disease, such as genome-wide association studies and candidate gene association studies. However, these statistical methods do not provide an understanding of the functional effects of variation...
March 13, 2017: Global Heart
https://www.readbyqxmd.com/read/28302399/elucidation-of-structural-and-functional-integration-of-a-novel-antimicrobial-peptide-from-antheraea-mylitta
#20
Suhrid R Dutta, Samiran S Gauri, Twisa Ghosh, Suman K Halder, Pradeep K DasMohapatra, Keshab C Mondal, Ananta K Ghosh
We report here the amino acid sequence of an antimicrobial peptide of Antheraea mylitta (peptide fraction II) effectively killed urinary tract associated MDR E. coli (Dutta et al., 2016), as Gly-Gly-Gly-Gly-Gly-Gly-His-Leu-Val-Ala. The physicochemical and biological properties of this peptide were evaluated by computational analysis and its isoelectric point, grand average of hydropathicity and Boman index values were found to be 6.74, 0.42 and -1.17kcal/mol, respectively. One valid model of peptide fraction II was constructed, that contains two antiparallel β sheets with a hairpin and appeared as 'U' shaped structure...
March 3, 2017: Bioorganic & Medicinal Chemistry Letters
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