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https://www.readbyqxmd.com/read/28735170/effects-of-different-solvents-on-the-conformations-of-apoptotic-cytochrome-c-structural-insights-from-molecular-dynamics-simulation
#1
Gurusamy Muneeswaran, Subramanian Kartheeswaran, Kaliappan Muthukumar, Christopher D Dharmaraj, Chandran Karunakaran
Cytochrome c (cyt-c) upon binding with cardiolipin acquires peroxidase activity and is strictly connected to the pathogenesis of many human diseases including neurodegenerative and cardiovascular diseases. Interaction of cyt-c with cardiolipin mimics partial unfolding/conformational changes of cyt-c in different solvent environments. Dynamic pictures of these conformational changes of cyt-c are crucial in understanding their physiological roles in mitochondrial functions. Therefore, atomistic molecular dynamics (MD) simulations have been carried out to investigate the effect of different solvents (water, urea/water, MeOH and DMSO) on the structure and conformations of apoptotic cyt-c (Fe(3+))...
July 14, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28735108/structural-biology-outside-the-box-inside-the-cell
#2
REVIEW
Jürgen M Plitzko, Benjamin Schuler, Philipp Selenko
Recent developments in cellular cryo-electron tomography, in-cell single-molecule Förster resonance energy transfer-spectroscopy, nuclear magnetic resonance-spectroscopy and electron paramagnetic resonance-spectroscopy delivered unprecedented insights into the inner workings of cells. Here, we review complementary aspects of these methods and provide an outlook toward joint applications in the future.
July 20, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28735107/integrative-modelling-of-cellular-assemblies
#3
REVIEW
Agnel Praveen Joseph, Guido Polles, Frank Alber, Maya Topf
A wide variety of experimental techniques can be used for understanding the precise molecular mechanisms underlying the activities of cellular assemblies. The inherent limitations of a single experimental technique often requires integration of data from complementary approaches to gain sufficient insights into the assembly structure and function. Here, we review popular computational approaches for integrative modelling of cellular assemblies, including protein complexes and genomic assemblies. We provide recent examples of integrative models generated for such assemblies by different experimental techniques, especially including data from 3D electron microscopy (3D-EM) and chromosome conformation capture experiments, respectively...
July 20, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28734665/potential-peptidic-proteasome-inhibitors-by-incorporation-of-an-electrophilic-trap-based-on-amino-acid-derived-%C3%AE-substituted-sulfonyl-fluorides
#4
Natalia Herrero Alvarez, Helmus van de Langemheen, Arwin J Brouwer, Rob M J Liskamp
Peptido sulfonyl fluoride derivatives were designed and synthesized containing a substituent on the alpha position (αPSFs) with respect to the sulfonyl fluoride electrophilic trap. The chemical reactivity of these α-substituted amino sulfonyl fluorides was studied and compared with the previously described β-substituted amino sulfonyl fluorides in order to get a deeper insight into the importance of the immediate structural environment of the sulfonyl fluoride moiety. Unfortunately, the poor solubility of the resulting αPSFs precluded a proper evaluation of their biological activity...
July 12, 2017: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/28734245/azaphenothiazines-promising-phenothiazine-derivatives-an-insight-into-nomenclature-synthesis-structure-elucidation-and-biological-properties
#5
REVIEW
Krystian Pluta, Małgorzata Jeleń, Beata Morak-Młodawska, Michał Zimecki, Jolanta Artym, Maja Kocięba, Ewa Zaczyńska
For the last two decades, classical phenothiazines have attracted attention of researchers, as the hitherto investigations have revealed many significant biological activities within this class of compounds, other than originally discovered neuroleptic ones. Important, new pharmaceutical results on phenothiazines, as 10-substituted dibenzothiazines, were recently highlighted in several reviews. Azaphenothiazines are structurally modified phenothiazines by substitution of one or both benzene rings in the phenothiazine ring system with the azine rings, such as: pyridine, pyridazine, pyrimidine, pyrazine, 1,2,4-triazine, quinoline, quinoxaline, benzoxazine and benzothiazine...
July 8, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28734209/new-insight-into-the-environmental-impact-of-two-imidazolium-ionic-liquids-effects-on-seed-germination-and-soil-microbial-activity
#6
J Salgado, J J Parajó, T Teijeira, O Cruz, J Proupín, M Villanueva, J A Rodríguez-Añón, P V Verdes, O Reyes
The next generation of ionic liquids must be synthetized taking into account structures that guarantee the suitable properties for a defined application as well as ecological data. Thus, searching of the right methodologies to know, quickly and efficiently, the ecological effects of these compounds is a preliminary task. The effects of two imidazolium based ionic liquids with different anions, 1-butyl-3-methylimidazolium tetrafluoroborate, [C4C1Im][BF4], and 1-propyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide, [C3C1Im][NTf2], on seedling emergence of six tree species and on the microbial behaviour of two soils were determined in this work...
July 14, 2017: Chemosphere
https://www.readbyqxmd.com/read/28734205/identification-of-mycobacterium-tuberculosis-enoyl-acyl-carrier-protein-reductase-inhibitors-a-combined-in-silico-and-in-vitro-analysis
#7
Mohsin Y Lone, Mohd Athar, Vivek K Gupta, Prakash C Jha
Mycobacterium tuberculosis (Mtb), had developed evolutionary changes in its genome to adapt for survival and thereby generated multi-drug resistant strains. However, novel drug targets that remained unchanged for their biochemical role has impressed the research community to target such proteins. The comprehensive analysis of multiple protein targets has influenced us to make a consensus structural rule exploited by pharmacophore and other allied techniques from a large repository of protein structures. In this pursuit, we made a retrospective analysis of pharmacophores mapped from the tuberculosis structural proteome and identified unique patterns that can be employed for the novel molecules design...
July 14, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28733859/the-past-and-future-in-understanding-the-health-risks-of-and-responses-to-climate-variability-and-change
#8
Kristie L Ebi, Jeremy J Hess
Climate change and health was established as a formal field of endeavor in the early 1990s, with the number of publications increasing since the mid-2000s. The key findings in assessment reports from the Intergovernmental Panel on Climate Change in 1995, 2001, 2007, and 2014 indicate the progress in understanding the magnitude and pattern of the health risks of a changing climate. The assessments maintained a similar structure, focusing on assessing the state of knowledge of individual climate-sensitive health outcomes, with confidence in the key findings tending to increase over time with greater understanding...
July 21, 2017: International Journal of Biometeorology
https://www.readbyqxmd.com/read/28733833/neuroanatomy-of-pain-deficiency-and-cross-modal-activation-in-calcium-channel-subunit-cacn-%C3%AE-2%C3%AE-3-knockout-mice
#9
Julia Landmann, Franziska Richter, Ana-Maria Oros-Peusquens, N Jon Shah, Joseph Classen, G Gregory Neely, Angelika Richter, Josef M Penninger, Ingo Bechmann
The phenotype of calcium channel subunit (CACN) α2δ3 knockout (KO) mice includes sensory cross-activation and deficient pain perception. Sensory cross-activation defines the activation of a sensory cortical region by input from another modality due to reorganization in the brain such as after sensory loss. To obtain mechanistic insight into both phenomena, we employed a comprehensive battery of neuroanatomical techniques. While CACNα2δ3 was ubiquitously expressed in wild-type mice, it was absent in α2δ3 KO animals...
July 21, 2017: Brain Structure & Function
https://www.readbyqxmd.com/read/28733658/structural-and-functional-analysis-of-latex-clearing-protein-lcp-provides-insight-into-the-enzymatic-cleavage-of-rubber
#10
Lorena Ilcu, Wolf Röther, Jakob Birke, Anton Brausemann, Oliver Einsle, Dieter Jendrossek
Latex clearing proteins (Lcps) are rubber oxygenases that catalyse the extracellular cleavage of poly (cis-1,4-isoprene) by Gram-positive rubber degrading bacteria. Lcp of Streptomyces sp. K30 (LcpK30) is a b-type cytochrome and acts as an endo-type dioxygenase producing C20 and higher oligo-isoprenoids that differ in the number of isoprene units but have the same terminal functions, CHO-CH2- and -CH2-COCH3. Our analysis of the LcpK30 structure revealed a 3/3 globin fold with additional domains at the N- and C-termini and similarities to globin-coupled sensor proteins...
July 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28733641/influence-of-c-terminal-truncation-of-murine-serum-amyloid-a-on-fibril-structure
#11
Matthies Rennegarbe, Inga Lenter, Angelika Schierhorn, Romy Sawilla, Christian Haupt
Amyloid A (AA) amyloidosis is a systemic protein misfolding disease affecting humans and other vertebrates. While the protein precursor in humans and mice is the acute-phase reactant serum amyloid A (SAA) 1.1, the deposited fibrils consist mainly of C-terminally truncated SAA fragments, termed AA proteins. For yet unknown reasons, phenotypic variations in the AA amyloid distribution pattern are clearly associated with specific AA proteins. Here we describe a bacterial expression system and chromatographic strategies to obtain significant amounts of C-terminally truncated fragments of murine SAA1...
July 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28733623/crystal-structure-of-a-low-molecular-weight-activator-blm-pep-with-yeast-20s-proteasome-insights-into-the-enzyme-activation-mechanism
#12
Julia Witkowska, Małgorzata Giżyńska, Przemysław Grudnik, Przemysław Golik, Przemysław Karpowicz, Artur Giełdoń, Grzegorz Dubin, Elżbieta Jankowska
Proteasomes are responsible for protein turnover in eukaryotic cells, degrading short-lived species but also removing improperly folded or oxidatively damaged ones. Dysfunction of a proteasome results in gradual accumulation of misfolded/damaged proteins, leading to their aggregation. It has been postulated that proteasome activators may facilitate removal of such aggregation-prone proteins and thus prevent development of neurodegenerative disorders. However, the discovery of pharmacologically relevant compounds is hindered by insufficient structural understanding of the activation process...
July 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28733604/the-n-terminal-dimerization-is-required-for-tdp-43-splicing-activity
#13
Lei-Lei Jiang, Wei Xue, Jun-Ye Hong, Jun-Ting Zhang, Min-Jun Li, Shao-Ning Yu, Jian-Hua He, Hong-Yu Hu
TDP-43 is a nuclear factor that functions in promoting pre-mRNA splicing. Deletion of the N-terminal domain (NTD) and nuclear localization signal (NLS) (i.e., TDP-35) results in mislocalization to cytoplasm and formation of inclusions. However, how the NTD functions in TDP-43 activity and proteinopathy remains largely unknown. Here, we studied the structure and function of the NTD in inclusion formation and pre-mRNA splicing of TDP-43 by using biochemical and biophysical approaches. We found that TDP-43 NTD forms a homodimer in solution in a concentration-dependent manner, and formation of intermolecular disulfide results in further tetramerization...
July 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28733581/structural-determinants-at-the-m2-muscarinic-receptor-modulate-the-rgs4-girk-response-to-pilocarpine-by-impairment-of-the-receptor-voltage-sensitivity
#14
I-Shan Chen, Kazuharu Furutani, Yoshihisa Kurachi
Membrane potential controls the response of the M2 muscarinic receptor to its ligands. Membrane hyperpolarization increases response to the full agonist acetylcholine (ACh) while decreasing response to the partial agonist pilocarpine. We previously have demonstrated that the regulator of G-protein signaling (RGS) 4 protein discriminates between the voltage-dependent responses of ACh and pilocarpine; however, the underlying mechanism remains unclear. Here we show that RGS4 is involved in the voltage-dependent behavior of the M2 muscarinic receptor-mediated signaling in response to pilocarpine...
July 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28733449/mitochondrial-function-in-engineered-cardiac-tissues-is-co-regulated-by-extracellular-matrix-elasticity-and-tissue-alignment
#15
Davi Marco Lyra-Leite, Allen Mariano Andres, Andrew Patrick Petersen, Nethika Ruvini Ariyasinghe, Nathan Cho, Jezell Athena Lee, Roberta A Gottlieb, Megan L McCain
Mitochondria in cardiac myocytes are critical for generating ATP to meet the high metabolic demands associated with sarcomere shortening. Distinct remodeling of mitochondrial structure and function occur in cardiac myocytes in both developmental and pathological settings. However, the factors that underlie these changes are poorly understood. Because remodeling of tissue architecture and extracellular matrix (ECM) elasticity are also hallmarks of ventricular development and disease, we hypothesize that these environmental factors regulate mitochondrial function in cardiac myocytes...
July 21, 2017: American Journal of Physiology. Heart and Circulatory Physiology
https://www.readbyqxmd.com/read/28733281/structural-and-mechanistic-insights-into-the-improvement-of-halotolerant-ability-of-a-marine-microbial-esterase-by-increasing-intra-and-inter-domain-hydrophobic-interactions
#16
Ping-Yi Li, Yi Zhang, Bin-Bin Xie, Yan-Qi Zhang, Jie Hao, Yue Wang, Peng Wang, Chun-Yang Li, Qi-Long Qin, Xi-Ying Zhang, Hai-Nan Su, Mei Shi, Yu-Zhong Zhang, Xiu-Lan Chen
Halotolerant enzymes are beneficial for industrial processes requiring high salts and low water activity. Most halophilic proteins are evolved to have reduced hydrophobic interactions on the surface and in the hydrophobic cores for their haloadaptation. However, in this study, we improved the halotolerance of a thermolablie esterase, E40, by increasing intra-protein hydrophobic interactions. E40 was quite unstable in buffers containing more than 0.3 M NaCl and its kcat and substrate affinity were both significantly reduced in 0...
July 21, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28733187/a-confidence-building-exercise-in-data-and-identifiability-modeling-cancer-chemotherapy-as-a-case-study
#17
Marisa C Eisenberg, Harsh V Jain
Mathematical modeling has a long history in the field of cancer therapeutics, and there is increasing recognition that it can help uncover the mechanisms that underlie tumor response to treatment. However, making quantitative predictions with such models often requires parameter estimation from data, raising questions of parameter identifiability and estimability. Even in the case of structural (theoretical) identifiability, imperfect data and the resulting practical unidentifiability of model parameters can make it difficult to infer the desired information, and in some cases, to yield biologically correct inferences and predictions...
July 18, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28733116/a-bright-future-for-serial-femtosecond-crystallography-with-xfels
#18
REVIEW
Linda C Johansson, Benjamin Stauch, Andrii Ishchenko, Vadim Cherezov
X-ray free electron lasers (XFELs) have the potential to revolutionize macromolecular structural biology due to the unique combination of spatial coherence, extreme peak brilliance, and short duration of X-ray pulses. A recently emerged serial femtosecond (fs) crystallography (SFX) approach using XFEL radiation overcomes some of the biggest hurdles of traditional crystallography related to radiation damage through the diffraction-before-destruction principle. Intense fs XFEL pulses enable high-resolution room-temperature structure determination of difficult-to-crystallize biological macromolecules, while simultaneously opening a new era of time-resolved structural studies...
July 18, 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/28732250/structural-biology-of-telomerase-and-its-interaction-at-telomeres
#19
REVIEW
Yaqiang Wang, Juli Feigon
Telomerase is an RNP that synthesizes the 3' ends of linear chromosomes and is an important regulator of telomere length. It contains a single long non-coding telomerase RNA (TER), telomerase reverse transcriptase (TERT), and other proteins that vary among organisms. Recent progress in structural biology of telomerase includes reports of the first cryo-electron microscopy structure of telomerase, from Tetrahymena, new crystal structures of TERT domains, telomerase RNA structures and models, and identification in Tetrahymena telomerase holoenzyme of human homologues of telomere-associated proteins that have provided a more unified view of telomerase interaction at telomeres as well as insights into the role of telomerase RNA in activity and assembly...
July 18, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28732246/inspiration-from-heart-development-biomimetic-development-of-functional-human-cardiac-organoids
#20
Dylan J Richards, Robert C Coyle, Yu Tan, Jia Jia, Kerri Wong, Katelynn Toomer, Donald R Menick, Ying Mei
Recent progress in human organoids has provided 3D tissue systems to model human development, diseases, as well as develop cell delivery systems for regenerative therapies. While direct differentiation of human embryoid bodies holds great promise for cardiac organoid production, intramyocardial cell organization during heart development provides biological foundation to fabricate human cardiac organoids with defined cell types. Inspired by the intramyocardial organization events in coronary vasculogenesis, where a diverse, yet defined, mixture of cardiac cell types self-organizes into functional myocardium in the absence of blood flow, we have developed a defined method to produce scaffold-free human cardiac organoids that structurally and functionally resembled the lumenized vascular network in the developing myocardium, supported hiPSC-CM development and possessed fundamental cardiac tissue-level functions...
July 12, 2017: Biomaterials
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