keyword
MENU ▼
Read by QxMD icon Read
search

Protein dynamic

keyword
https://www.readbyqxmd.com/read/29454111/combining-rosetta-with-molecular-dynamics-md-a-benchmark-of-the-md-based-ensemble-protein-design
#1
Jan Ludwiczak, Adam Jarmula, Stanislaw Dunin-Horkawicz
Computational protein design is a set of procedures for computing amino acid sequences that will fold into a specified structure. Rosetta Design, a commonly used software for protein design, allows for the effective identification of sequences compatible with a given backbone structure, while molecular dynamics (MD) simulations can thoroughly sample near-native conformations. We benchmarked a procedure in which Rosetta design is started on MD-derived structural ensembles and showed that such a combined approach generates 20 to 30% more diverse sequences than currently available methods with only a slight increase in computation time...
February 14, 2018: Journal of Structural Biology
https://www.readbyqxmd.com/read/29453971/prediction-value-of-serum-hbv-large-surface-protein-in-different-phases-of-hbv-infection-and-virological-response-of-chronic-hepatitis-b-patients
#2
Can Liu, Wennan Wu, Hongyan Shang, Sheng Lin, Zhen Xun, Er Huang, Jinpiao Lin, Bin Yang, Qishui Ou
BACKGROUND: Serum HBV large surface protein (HBV-LP) is an envelope protein that has a close relationship with HBV DNA level. This study is to explore the prediction value of HBV-LP in different phase of HBV infection and during antiviral therapy in chronic hepatitis B (CHB) patients. METHODS: A retrospective study was conducted in 2033 individuals, which included 1677 HBV infected patients in different phases and 356 healthy controls. HBV-LP, HBV serum markers and HBV DNA were detected by ELISA, CMIA and qRT-PCR, respectively...
February 14, 2018: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/29453948/noncritical-signaling-role-of-a-kinase-receptor-interaction-surface-in-the-escherichia-coli-chemosensory-core-complex
#3
Germán E Piñas, Michael D DeSantis, John S Parkinson
In E. coli chemosensory arrays, transmembrane receptors, a histidine autokinase CheA, and a scaffolding protein CheW interact to form an extended hexagonal lattice of signaling complexes. One interaction, previously assigned a crucial signaling role, occurs between chemoreceptors and the CheW-binding P5 domain of CheA. Structural studies showed a receptor helix fitting into a hydrophobic cleft at the boundary between P5 subdomains. Our work aimed to elucidate the in vivo roles of the receptor-P5 interface, employing as a model the interaction between E...
February 14, 2018: Journal of Molecular Biology
https://www.readbyqxmd.com/read/29453713/-1-h-13-c-and-15-n-resonance-assignments-of-cw-domain-of-the-n-methyltransferase-ashh2-free-and-bound-to-the-mono-di-and-tri-methylated-histone-h3-tail-peptides
#4
Olena Dobrovolska, Maxim Bril'kov, Øyvind Ødegård-Fougner, Rein Aasland, Øyvind Halskau
The ASHH2 CW domain is responsible for recognizing the methylation state at lysine 4 of histone 3 N-terminal tails and implicated in the recruitment of the ASHH2 methyltransferase enzyme correctly to the histones. The ASHH2 CW domain binds H3 lysine motifs that can be either mono-, di-, or tri-methylated [ARTK(meX)QTAR, where X denotes the number of methylations], but binds strongest to monomethylated instances (K d values reported in the range of 1 µm to 500 nM). Hoppmann et al. published the uncomplexed NMR structure of an ASHH2 CW domain in 2011...
February 16, 2018: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/29453691/effect-of-phosphorylation-and-single-nucleotide-polymorphisms-on-caspase-substrates-processing
#5
Sonu Kumar, Piotr Cieplak
Posttranslational modifications that involve either reversible covalent modification of proteins or irreversible proteolysis are central to the regulation of key cellular mechanisms, including apoptosis, cell-cycle regulation and signal transduction. There is mounting evidence suggesting cross-talk between proteases and kinases. For instance: caspases, a class of proteases involved in programmed cell death-apoptosis, cleave a large set of various types of proteins. Simultaneously, kinases restrict caspase activity by phosphorylating their protein substrates in the vicinity of cleavage site...
February 16, 2018: Apoptosis: An International Journal on Programmed Cell Death
https://www.readbyqxmd.com/read/29453575/regulation-of-blood-testis-barrier-btb-dynamics-role-of-actin-and-microtubule-based-cytoskeletons
#6
Qing Wen, Elizabeth I Tang, Nan Li, Dolores D Mruk, Will M Lee, Bruno Silvestrini, C Yan Cheng
The blood-testis barrier (BTB) is an important ultrastructure in the testis that supports meiosis and postmeiotic spermatid development since a delay in the establishment of a functional Sertoli cell barrier during postnatal development in rats or mice by 17-20 day postpartum (dpp) would lead to a delay of the first wave of meiosis. Furthermore, irreversible disruption of the BTB by toxicants also induces infertility in rodents. Herein, we summarize recent findings that BTB dynamics (i.e., disassembly, reassembly, and stabilization) are supported by the concerted efforts of the actin- and microtubule (MT)-based cytoskeletons...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29453312/inhibition-of-ras-activity-coordinates-cell-fusion-with-cell-cell-contact-during-yeast-mating
#7
Laura Merlini, Bita Khalili, Omaya Dudin, Laetitia Michon, Vincent Vincenzetti, Sophie G Martin
In the fission yeast Schizosaccharomyces pombe , pheromone signaling engages a signaling pathway composed of a G protein-coupled receptor, Ras, and a mitogen-activated protein kinase (MAPK) cascade that triggers sexual differentiation and gamete fusion. Cell-cell fusion requires local cell wall digestion, which relies on an initially dynamic actin fusion focus that becomes stabilized upon local enrichment of the signaling cascade on the structure. We constructed a live-reporter of active Ras1 (Ras1-guanosine triphosphate [GTP]) that shows Ras activity at polarity sites peaking on the fusion structure before fusion...
February 16, 2018: Journal of Cell Biology
https://www.readbyqxmd.com/read/29452937/epigenetic-chromatin-modification-by-amber-suppression-technology
#8
REVIEW
Heinz Neumann, Petra Neumann-Staubitz, Anna Witte, Daniel Summerer
The genetic incorporation of unnatural amino acids (UAAs) into proteins by amber suppression technology provides unique avenues to study protein structure, function and interactions both in vitro and in living cells and organisms. This approach has been particularly useful for studying mechanisms of epigenetic chromatin regulation, since these extensively involve dynamic changes in structure, complex formation and posttranslational modifications that are difficult to access by traditional approaches. Here, we review recent achievements in this field, emphasizing UAAs that help to unravel protein-protein interactions in cells by photo-crosslinking or that allow the biosynthesis of proteins with defined posttranslational modifications for studying their function and turnover in vitro and in cells...
February 13, 2018: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/29452577/polymerase-delta-interacting-protein-2-deficiency-protects-against-blood-brain-barrier-permeability-in-the-ischemic-brain
#9
Marina S Hernandes, Bernard Lassègue, Lula L Hilenski, Jonathan Adams, Ning Gao, Chia-Yi Kuan, Yu-Yo Sun, Lihong Cheng, Daniel S Kikuchi, Manuel Yepes, Kathy K Griendling
BACKGROUND: Polymerase δ-interacting protein 2 (Poldip2) is a multifunctional protein that regulates vascular extracellular matrix composition and matrix metalloproteinase (MMP) activity. The blood-brain barrier (BBB) is a dynamic system assembled by endothelial cells, basal lamina, and perivascular astrocytes, raising the possibility that Poldip2 may be involved in maintaining its structure. We investigated the role of Poldip2 in the late BBB permeability induced by cerebral ischemia...
February 17, 2018: Journal of Neuroinflammation
https://www.readbyqxmd.com/read/29452382/simulated-ablation-for-detection-of-cells-impacting-paracrine-signalling-in-histology-analysis
#10
Jake P Taylor-King, Etienne Baratchart, Andrew Dhawan, Elizabeth A Coker, Inga Hansine Rye, Hege Russnes, S Jon Chapman, David Basanta, Andriy Marusyk
Intra-tumour phenotypic heterogeneity limits accuracy of clinical diagnostics and hampers the efficiency of anti-cancer therapies. Dealing with this cellular heterogeneity requires adequate understanding of its sources, which is extremely difficult, as phenotypes of tumour cells integrate hardwired (epi)mutational differences with the dynamic responses to microenvironmental cues. The later comes in form of both direct physical interactions, as well as inputs from gradients of secreted signalling molecules. Furthermore, tumour cells can not only receive microenvironmental cues, but also produce them...
February 14, 2018: Mathematical Medicine and Biology: a Journal of the IMA
https://www.readbyqxmd.com/read/29452267/git2-a-keystone-in-ageing-and-age-related-disease
#11
REVIEW
Jaana van Gastel, Jan Boddaert, Areta Jushaj, Richard T Premont, Louis M Luttrell, Jonathan Janssens, Bronwen Martin, Stuart Maudsley
Since its discovery, G protein-coupled receptor kinase-interacting protein 2, GIT2, and its family member, GIT1, have received considerable interest concerning their potential key roles in regulating multiple inter-connected physiological and pathophysiological processes. GIT2 was first identified as a multifunctional protein that is recruited to G protein-coupled receptors (GPCRs) during the process of receptor internalization. Recent findings have demonstrated that perhaps one of the most important effects of GIT2 in physiology concerns its role in controlling multiple aspects of the complex ageing process...
February 13, 2018: Ageing Research Reviews
https://www.readbyqxmd.com/read/29451901/the-novel-antibiotic-rhodomyrtone-traps-membrane-proteins-in-vesicles-with-increased-fluidity
#12
Dennapa Saeloh, Varomyalin Tipmanee, Kin Ki Jim, Marien P Dekker, Wilbert Bitter, Supayang P Voravuthikunchai, Michaela Wenzel, Leendert W Hamoen
The acylphloroglucinol rhodomyrtone is a promising new antibiotic isolated from the rose myrtle Rhodomyrtus tomentosa, a plant used in Asian traditional medicine. While many studies have demonstrated its antibacterial potential in a variety of clinical applications, very little is known about the mechanism of action of rhodomyrtone. Preceding studies have been focused on intracellular targets, but no specific intracellular protein could be confirmed as main target. Using live cell, high-resolution, and electron microscopy we demonstrate that rhodomyrtone causes large membrane invaginations with a dramatic increase in fluidity, which attract a broad range of membrane proteins...
February 16, 2018: PLoS Pathogens
https://www.readbyqxmd.com/read/29451771/structural-transformation-of-wireframe-dna-origami-via-dna-polymerase-assisted-gap-filling
#13
Nayan P Agarwal, Michael Matthies, Bastian Joffroy, Thorsten L Schmidt
The programmability of DNA enables constructing nanostructures with almost any arbitrary shape, which can be decorated with many functional materials. Moreover, dynamic structures can be realized such as molecular motors and walkers. In this work, we have explored the possibility to synthesize the complementary sequences to single-stranded gap regions in the DNA origami scaffold cost effectively by a DNA polymerase rather than by a DNA synthesizer. For this purpose, four different wireframe DNA origami structures were designed to have single-stranded gap regions...
February 16, 2018: ACS Nano
https://www.readbyqxmd.com/read/29451494/single-cell-transcriptional-dynamics-of-flavivirus-infection
#14
Fabio Zanini, Szu-Yuan Pu, Elena Bekerman, Shirit Einav, Stephen R Quake
Dengue and Zika viral infections affect millions of people annually and can be complicated by hemorrhage or neurological manifestations, respectively. However, a thorough understanding of the host response to these viruses is lacking, partly because conventional approaches ignore heterogeneity in virus abundance across cells. We present viscRNA-Seq (virus-inclusive single cell RNA-Seq), an approach to probe the host transcriptome together with intracellular viral RNA at the single cell level. We applied viscRNA-Seq to monitor dengue and Zika virus infection in cultured cells and discovered extreme heterogeneity in virus abundance...
February 16, 2018: ELife
https://www.readbyqxmd.com/read/29450991/mass-spectrometry-based-fast-photochemical-oxidation-of-proteins-fpop-for-higher-order-structure-characterization
#15
Ke Sherry Li, Liuqing Shi, Michael L Gross
Assessment of protein structure and interaction is crucial for understanding protein structure/function relationships. Compared to high-resolution structural tools, including X-ray crystallography, nuclear magnetic resonance (NMR), and cryo-EM, and traditional low-resolution methods, such as circular dichroism, UV-vis, and florescence spectroscopy, mass spectrometry (MS)-based protein footprinting affords medium-to-high resolution (i.e., regional and residue-specific insights) by taking advantage of proteomics methods focused on the primary structure...
February 16, 2018: Accounts of Chemical Research
https://www.readbyqxmd.com/read/29450849/impaired-arterial-responsiveness-in-untreated-gout-patients-compared-with-healthy-non-gout-controls-association-with-serum-urate-and-c-reactive-protein
#16
Svetlana Krasnokutsky, Aaron Garza Romero, Daisy Bang, Virginia C Pike, Binita Shah, Talia F Igel, Irina Dektiarev, Yu Guo, Judy Zhong, Stuart D Katz, Michael H Pillinger
To determine whether arterial responsiveness is impaired among patients with gout, and whether arterial responsiveness inversely correlates with serum urate and inflammatory measures. This is a cross-sectional study of untreated gout subjects (n = 34) and non-gout healthy controls (n = 64). High-resolution dynamic ultrasound-measured flow-mediated dilation (FMD) and nitroglycerin-mediated dilation (NMD) assessed endothelium-dependent and endothelium-independent arterial responsiveness respectively. Serum urate (sUA) and high-sensitivity C-reactive protein (hsCRP) were measured in the gout group, and correlated with FMD and NMD responses...
February 15, 2018: Clinical Rheumatology
https://www.readbyqxmd.com/read/29450823/nmr-resonance-assignments-of-rnase-p-protein-from-thermotoga-maritima
#17
Danyun Zeng, Benjamin P Brown, Markus W Voehler, Sheng Cai, Nicholas J Reiter
Ribonuclase P (RNase P) is an essential metallo-endonuclease that catalyzes 5' precursor-tRNA (ptRNA) processing and exists as an RNA-based enzyme in bacteria, archaea, and eukaryotes. In bacteria, a large catalytic RNA and a small protein component assemble to recognize and accurately cleave ptRNA and tRNA-like molecular scaffolds. Substrate recognition of ptRNA by bacterial RNase P requires RNA-RNA shape complementarity, intermolecular base pairing, and a dynamic protein-ptRNA binding interface. To gain insight into the binding specificity and dynamics of the bacterial protein-ptRNA interface, we report the backbone and side chain 1 H, 13 C, and 15 N resonance assignments of the hyperthermophilic Thermatoga maritima RNase P protein in solution at 318 K...
February 15, 2018: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/29450541/induction-of-ocular-complement-activation-by-inflammatory-stimuli-and-intraocular-inhibition-of-complement-factor-d-in-animal-models
#18
Maura A Crowley, Omar Delgado, Adrian Will-Orrego, Natasha M Buchanan, Karen Anderson, Bruce D Jaffee, Thaddeus P Dryja, Sha-Mei Liao
Purpose: Genome-wide association studies suggest a role for the complement system in age-related macular degeneration (AMD). We characterized ocular complement activation and evaluated a complement factor D (FD) neutralizing antibody. Methods: Mice were treated with toll-like receptor (TLR) ligands, intravitreal injection (IVT), or corneal debridement. Levels of complement proteins and mRNA were measured. A FD neutralizing antibody was administered IVT into eyes of rabbits that were challenged with LPS (lipopolysaccharide) administered intravenously...
February 1, 2018: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/29450111/the-binding-structure-and-affinity-of-photodamaged-duplex-dna-with-members-of-the-photolyase-cryptochrome-family-a-computational-study
#19
Ryuma Sato, Ryuhei Harada, Yasuteru Shigeta
Photolyases (PHRs) and cryptochromes (CRYs) belong to the same family known as blue-light photoreceptors. Although their amino acid sequences and corresponding structures are similar to each other, they exert different functions. PHRs function as an enzyme to repair UV-induced deoxyribonucleic acid (DNA) lesions such as a cyclobutane pyrimidine dimer (CPD) and a (6-4) photoproduct ((6-4)pp), whereas CRYs are a circadian photoreceptor in plants and animals and at the same time they control the photoperiodic induction of flowering in plants...
2018: Biophysics and Physicobiology
https://www.readbyqxmd.com/read/29450109/determination-of-diffusion-coefficients-in-live-cells-using-fluorescence-recovery-after-photobleaching-with-wide-field-fluorescence-microscopy
#20
Akira Kitamura, Masataka Kinjo
Fluorescence recovery after photobleaching (FRAP) enables characterization of quantitative dynamic properties such as diffusion coefficients of fluorescent molecules in living cells by analyzing the recovery of fluorescence intensity after photobleaching in a specific cellular compartment or area. To quantitatively determine high intracellular diffusion coefficients, a suitable optical system as well as an appropriate model for fast diffusion analysis is necessary. Here, we propose a procedure to quantify the diffusion coefficient of rapidly-diffusing fluorescent molecules that makes use of an epi-fluorescence microscope with a photobleaching laser in combination with established models for diffusion analysis...
2018: Biophysics and Physicobiology
keyword
keyword
64848
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"