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https://www.readbyqxmd.com/read/28538145/nmr-analysis-of-amide-hydrogen-exchange-rates-in-a-pentapeptide-repeat-protein-from-a-%C3%A2-thaliana
#1
Shenyuan Xu, Shuisong Ni, Michael A Kennedy
At2g44920 from Arabidopsis thaliana is a pentapeptide-repeat protein (PRP) composed of 25 repeats capped by N- and C-terminal α-helices. PRP structures are dominated by four-sided right-handed β-helices typically consisting of mixtures of type II and type IV β-turns. PRPs adopt repeated five-residue (Rfr) folds with an Rfr consensus sequence (STAV)(D/N)(L/F)(S/T/R)(X). Unlike other PRPs, At2g44920 consists exclusively of type II β-turns. At2g44920 is predicted to be located in the thylakoid lumen although its biochemical function remains unknown...
May 23, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28538142/an-introduction-to-infinite-hmms-for-single-molecule-data-analysis
#2
REVIEW
Ioannis Sgouralis, Steve Pressé
The hidden Markov model (HMM) has been a workhorse of single-molecule data analysis and is now commonly used as a stand-alone tool in time series analysis or in conjunction with other analysis methods such as tracking. Here, we provide a conceptual introduction to an important generalization of the HMM, which is poised to have a deep impact across the field of biophysics: the infinite HMM (iHMM). As a modeling tool, iHMMs can analyze sequential data without a priori setting a specific number of states as required for the traditional (finite) HMM...
May 23, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28537745/deciphering-cryptic-binding-sites-on-proteins-by-mixed-solvent-molecular-dynamics
#3
S Roy Kimura, Haipeng Hu, Anatoly M Ruvinsky, Woody B Sherman, Angelo D Favia
In recent years, molecular dynamics simulations of proteins in explicit mixed-solvents have been applied to various problems in protein biophysics and drug discovery, including protein folding, protein surface characterization, fragment screening, allostery, and druggability assessment. In this study, we perform a systematic study on how mixtures of organic solvent probes in water can reveal cryptic ligand binding pockets that are not evident in crystal structures of apo proteins. We examine a diverse set of eight PDB proteins that show pocket opening induced by ligand binding and investigate whether solvent MD simulations on the apo structures can induce the binding site observed in the holo structures...
May 24, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28537726/hot-spotting-with-thermal-scanning-a-ligand-and-structure-independent-assessment-of-target-ligandability
#4
Molly Chilton, Ben Clennell, Fredrik Edfeldt, Stefan Geschwindner
Evaluating the ligandability of a protein target is a key component when defining hit-finding strategies or to prioritize amongst drug targets. Computational as well as biophysical approaches based on nuclear magnetic resonance (NMR) fragment screening are powerful approaches, but suffer from specific constraints that limit their usage. Here, we demonstrate the applicability of high-throughput thermal scanning (HTTS) as a simple and generic biophysical fragment screening method to reproduce assessments from NMR-based screening...
May 24, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28534491/structural-basis-for-perception-of-diverse-chemical-substances-by-t1r-taste-receptors
#5
Nipawan Nuemket, Norihisa Yasui, Yuko Kusakabe, Yukiyo Nomura, Nanako Atsumi, Shuji Akiyama, Eriko Nango, Yukinari Kato, Mika K Kaneko, Junichi Takagi, Maiko Hosotani, Atsuko Yamashita
The taste receptor type 1 (T1r) family perceives 'palatable' tastes. These receptors function as T1r2-T1r3 and T1r1-T1r3 heterodimers to recognize a wide array of sweet and umami (savory) tastes in sugars and amino acids. Nonetheless, it is unclear how diverse tastes are recognized by so few receptors. Here we present crystal structures of the extracellular ligand-binding domains (LBDs), the taste recognition regions of the fish T1r2-T1r3 heterodimer, bound to different amino acids. The ligand-binding pocket in T1r2LBD is rich in aromatic residues, spacious and accommodates hydrated percepts...
May 23, 2017: Nature Communications
https://www.readbyqxmd.com/read/28534480/molecular-basis-for-primpol-recruitment-to-replication-forks-by-rpa
#6
Thomas A Guilliam, Nigel C Brissett, Aaron Ehlinger, Benjamin A Keen, Peter Kolesar, Elaine M Taylor, Laura J Bailey, Howard D Lindsay, Walter J Chazin, Aidan J Doherty
DNA damage and secondary structures can stall the replication machinery. Cells possess numerous tolerance mechanisms to complete genome duplication in the presence of such impediments. In addition to translesion synthesis (TLS) polymerases, most eukaryotic cells contain a multifunctional replicative enzyme called primase-polymerase (PrimPol) that is capable of directly bypassing DNA damage by TLS, as well as repriming replication downstream of impediments. Here, we report that PrimPol is recruited to reprime through its interaction with RPA...
May 23, 2017: Nature Communications
https://www.readbyqxmd.com/read/28533371/blue-fluorescent-amino-acid-for-biological-spectroscopy-and-microscopy
#7
Mary Rose Hilaire, Ismail A Ahmed, Chun-Wei Lin, Hyunil Jo, William F DeGrado, Feng Gai
Many fluorescent proteins are currently available for biological spectroscopy and imaging measurements, allowing a wide range of biochemical and biophysical processes and interactions to be studied at various length scales. However, in applications where a small fluorescence reporter is required or desirable, the choice of fluorophores is rather limited. As such, continued effort has been devoted to the development of amino acid-based fluorophores that do not require a specific environment and additional time to mature and have a large fluorescence quantum yield, long fluorescence lifetime, good photostability, and an emission spectrum in the visible region...
May 22, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28532604/validation-of-dwi-pre-processing-procedures-for-reliable-differentiation-between-human-brain-gliomas
#8
Sebastian Vellmer, Aram S Tonoyan, Dieter Suter, Igor N Pronin, Ivan I Maximov
Diffusion magnetic resonance imaging (dMRI) is a powerful tool in clinical applications, in particular, in oncology screening. dMRI demonstrated its benefit and efficiency in the localisation and detection of different types of human brain tumours. Clinical dMRI data suffer from multiple artefacts such as motion and eddy-current distortions, contamination by noise, outliers etc. In order to increase the image quality of the derived diffusion scalar metrics and the accuracy of the subsequent data analysis, various pre-processing approaches are actively developed and used...
May 19, 2017: Zeitschrift Für Medizinische Physik
https://www.readbyqxmd.com/read/28532218/flow-chamber-and-microfluidic-approaches-for-measuring-thrombus-formation-in-genetic-bleeding-disorders
#9
Rogier M Schoeman, Marcus Lehmann, Keith B Neeves
Platelet adhesion and aggregation, coagulation, fibrin formation, and fibrinolysis are regulated by the forces and flows imposed by blood at the site of a vascular injury. Flow chambers designed to observe these events are an indispensable part of doing hemostasis and thrombosis research, especially with human blood. Microfluidic methods have provided the flexibility to design flow chambers with complex geometries and features that more closely mimic the anatomy and physiology of blood vessels. Additionally, microfluidic systems with integrated optics and/or pressure sensors and on-board signal processing could transform what have been primarily research tools into clinical assays...
May 22, 2017: Platelets
https://www.readbyqxmd.com/read/28531796/spatially-explicit-modeling-of-multi-scale-drivers-of-aboveground-forest-biomass-and-water-yield-in-watersheds-of-the-southeastern-united-states
#10
Mukhtar Ahmed Ajaz Ahmed, Amr Abd-Elrahman, Francisco J Escobedo, Wendell P Cropper, Timothy A Martin, Nilesh Timilsina
Understanding ecosystem processes and the influence of regional scale drivers can provide useful information for managing forest ecosystems. Examining more local scale drivers of forest biomass and water yield can also provide insights for identifying and better understanding the effects of climate change and management on forests. We used diverse multi-scale datasets, functional models and Geographically Weighted Regression (GWR) to model ecosystem processes at the watershed scale and to interpret the influence of ecological drivers across the Southeastern United States (SE US)...
May 19, 2017: Journal of Environmental Management
https://www.readbyqxmd.com/read/28530823/nanomechanically-visualizing-drug-cell-interaction-at-the-early-stage-of-chemotherapy
#11
Yun-Long Wu, Wilfried Engl, Benhui Hu, Pingqiang Cai, Wan Ru Leow, Nguan Soon Tan, Chwee Teck Lim, Xiaodong Chen
A detailed understanding of chemotherapy is determined by the response of cell to the formation of the drug-target complex and its corresponding sudden or eventual cell death. However, visualization of this early but important process, encompassing the fast dynamics as well as complex network of molecular pathways, remains challenging. Herein, we report that the nanomechanical traction force is sensitive enough to reflect the early cellular response upon the addition of chemotherapeutical molecules in a real-time and non-invasive manner, due to interactions between chemotherapeutic drug and its cytoskeleton targets...
May 22, 2017: ACS Nano
https://www.readbyqxmd.com/read/28530658/endoglin-controls-blood-vessel-diameter-through-endothelial-cell-shape-changes-in-response-to-haemodynamic-cues
#12
Wade W Sugden, Robert Meissner, Tinri Aegerter-Wilmsen, Roman Tsaryk, Elvin V Leonard, Jeroen Bussmann, Mailin J Hamm, Wiebke Herzog, Yi Jin, Lars Jakobsson, Cornelia Denz, Arndt F Siekmann
The hierarchical organization of properly sized blood vessels ensures the correct distribution of blood to all organs of the body, and is controlled via haemodynamic cues. In current concepts, an endothelium-dependent shear stress set point causes blood vessel enlargement in response to higher flow rates, while lower flow would lead to blood vessel narrowing, thereby establishing homeostasis. We show that during zebrafish embryonic development increases in flow, after an initial expansion of blood vessel diameters, eventually lead to vessel contraction...
May 22, 2017: Nature Cell Biology
https://www.readbyqxmd.com/read/28529725/the-catalytic-function-of-cytochrome-p450-is-entwined-with-its-membrane-bound-nature
#13
REVIEW
Carlo Barnaba, Katherine Gentry, Nirupama Sumangala, Ayyalusamy Ramamoorthy
Cytochrome P450, a family of monooxygenase enzymes, is organized as a catalytic metabolon, which requires enzymatic partners as well as environmental factors that tune its complex dynamic. P450 and its reducing counterparts-cytochrome P450-reductase and cytochrome b 5 -are membrane-bound proteins located in the cytosolic side of the endoplasmic reticulum. They are believed to dynamically associate to form functional complexes. Increasing experimental evidence signifies the role(s) played by both protein-protein and protein-lipid interactions in P450 catalytic function and efficiency...
2017: F1000Research
https://www.readbyqxmd.com/read/28529713/gap-junction-structure-unraveled-but-not-fully-revealed
#14
REVIEW
Eric C Beyer, Viviana M Berthoud
Gap junction channels facilitate the intercellular exchange of ions and small molecules, a process that is critical for the function of many different kinds of cells and tissues. Recent crystal structures of channels formed by one connexin isoform (connexin26) have been determined, and they have been subjected to molecular modeling. These studies have provided high-resolution models to gain insights into the mechanisms of channel conductance, molecular permeability, and gating. The models share similarities, but there are some differences in the conclusions reached by these studies...
2017: F1000Research
https://www.readbyqxmd.com/read/28529672/on-chip-density-based-purification-of-liposomes
#15
Siddharth Deshpande, Anthony Birnie, Cees Dekker
Due to their cell membrane-mimicking properties, liposomes have served as a versatile research tool in science, from membrane biophysics and drug delivery systems to bottom-up synthetic cells. We recently reported a novel microfluidic method, Octanol-assisted Liposome Assembly (OLA), to form cell-sized, monodisperse, unilamellar liposomes with excellent encapsulation efficiency. Although OLA provides crucial advantages over alternative methods, it suffers from the presence of 1-octanol droplets, an inevitable by-product of the production process...
May 2017: Biomicrofluidics
https://www.readbyqxmd.com/read/28529483/identification-of-a-novel-allosteric-inhibitory-site-on-tryptophan-hydroxylase-1-enabling-unprecedented-selectivity-over-all-related-hydroxylases
#16
Mike Petrassi, Rob Barber, Celine Be, Sarah Beach, Brian Cox, Anne-Marie D'Souza, Nick Duggan, Martin Hussey, Roy Fox, Peter Hunt, Gabor Jarai, Takatoshi Kosaka, Paul Oakley, Viral Patel, Neil Press, David Rowlands, Clemens Scheufler, Oliver Schmidt, Honnappa Srinivas, Mary Turner, Rob Turner, John Westwick, Alison Wolfreys, Nuzhat Pathan, Simon Watson, Matthew Thomas
Pulmonary arterial hypertension (PAH) has demonstrated multi-serotonin receptor dependent pathologies, characterized by increased tone (5-HT1B receptor) and complex lesions (SERT, 5-HT1B, 5-HT2B receptors) of the pulmonary vasculature together with right ventricular hypertrophy, ischemia and fibrosis (5-HT2B receptor). Selective inhibitors of individual signaling elements - SERT, 5-HT2A, 5HT2B, and combined 5-HT2A/B receptors, have all been tested clinically and failed. Thus, inhibition of tryptophan hydroxylase 1 (TPH1), the rate limiting step in 5-HT synthesis, has been suggested as a more broad, and thereby more effective, mode of 5-HT inhibition...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/28529337/dynamic-chromatin-technologies-from-individual-molecules-to-epigenomic-regulation-in-cells
#17
REVIEW
Olivier Cuvier, Beat Fierz
The establishment and maintenance of chromatin states involves multiscale dynamic processes integrating transcription factor and multiprotein effector dynamics, cycles of chemical chromatin modifications, and chromatin structural organization. Recent developments in genomic technologies are emerging that are enabling a view beyond ensemble- and time-averaged properties and are revealing the importance of dynamic chromatin states for cell fate decisions, differentiation and reprogramming at the single-cell level...
May 22, 2017: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/28528958/investigation-of-calcium-dependent-activity-and-conformational-dynamics-of-zebra-fish-12-lipoxygenase
#18
Monica Mittal, Mahmudul Hasan, Navisraj Balagunaseelan, Alexander Fauland, Craig Wheelock, Olof Rådmark, Jesper Z Haeggström, Agnes Rinaldo-Matthis
BACKGROUND: A 12-lipoxygenase in zebra fish (zf12-LOX) was found to be required for normal embryonic development and LOXs are of great interest for targeted drug designing. In this study, we investigate the structural-functional aspects of zf12-LOX in response to calcium. METHODS: A soluble version of zf12-LOX was created by mutagenesis. Based on multiple sequence alignment, we mutated the putative calcium-responsive amino acids in N-PLAT domain of soluble zf12-LOX...
May 18, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28528876/modeling-covalent-modifier-drugs
#19
REVIEW
Ernest Awoonor-Williams, Andrew G Walsh, Christopher N Rowley
In this review, we present a summary of how computer modeling has been used in the development of covalent modifier drugs. Covalent modifier drugs bind by forming a chemical bond with their target. This covalent binding can improve the selectivity of the drug for a target with complementary reactivity and result in increased binding affinities due to the strength of the covalent bond formed. In some cases, this results in irreversible inhibition of the target, but some targeted covalent inhibitor (TCI) drugs bind covalently but reversibly...
May 18, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28528849/extracellular-low-n-oligomers-of-tau-cause-selective-synaptotoxicity-without-affecting-cell-viability
#20
Senthilvelrajan Kaniyappan, Ram Reddy Chandupatla, Eva-Maria Mandelkow, Eckhard Mandelkow
INTRODUCTION: Tau-mediated toxicity in Alzheimer's disease is thought to operate through low-n oligomers, rather than filamentous aggregates. However, the nature of oligomers and pathways of toxicity are poorly understood. Therefore, we investigated structural and functional aspects of highly purified oligomers of a pro-aggregant tau species. METHODS: Purified oligomers of the tau repeat domain were characterized by biophysical and structural methods. Functional aspects were investigated by cellular assays ((3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium) bromide assay of cell viability, lactate dehydrogenase release assay [for cell toxicity], reactive oxygen species production, and calcium assay), combined with analysis of neuronal dendritic spines exposed to oligomers...
May 18, 2017: Alzheimer's & Dementia: the Journal of the Alzheimer's Association
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