keyword
MENU ▼
Read by QxMD icon Read
search

molecular dynamics

keyword
https://www.readbyqxmd.com/read/28648006/-0-5-gy-x-ray-radiation-promotes-osteoblast-differentiation-by-wnt-%C3%AE-catenin-signaling
#1
M Chen, Q R Dong, Q Huang, C She, W Xu
Objective: To investigate the important roles of Wnt signaling in the processes of 0.5Gy X-ray promoting osteoblast differentiation, and make clear the molecular mechanisms involved. Methods: Flow cytometry was employed to detect the apoptosis after osteoblast exposure to 0.5 Gy X-ray radiation.The protein level of osteoblast differentiation markers, such as collagen Iα (Col1α), alkaline phosphatase (ALP), osteocalcin (OCN), were detected by Western-blot and ALP activity staining was performed. Real-time PCR and Western-blot were utilized to evaluate the variations of key factors in Wnt signaling pathways, while specific inhibitor of Wnt/β-Catenin, XAV939 was used to block the Wnt signaling...
June 20, 2017: Zhonghua Yi Xue za Zhi [Chinese medical journal]
https://www.readbyqxmd.com/read/28647813/ghvln4-is-involved-in-cell-elongation-via-regulation-of-actin-organization
#2
Fenni Lv, Mingya Han, Dongdong Ge, Hui Dong, Xiaotong Zhang, Lifeng Li, Peipei Zhang, Zhongqi Zhang, Jing Sun, Kang Liu, Youlu Yuan
GhVLN4 exhibited activity of cross-linking actin filaments into bundles. Overexpression of GhVLN4 increased the abundance of thick actin bundles and resulted in longer cell phenotypes. Actin bundle is a dynamic, higher-order cytoskeleton structure that is essential for cell expansion. Villin is one of the major proteins responsible for crosslinking actin filaments into bundles. However, this kind of actin binding protein has rarely been investigated in cotton. In the present work, a cotton villin gene was molecularly cloned from Upland cotton and denominated as GhVLN4...
June 24, 2017: Planta
https://www.readbyqxmd.com/read/28647693/recognition-investigation-and-management-of-mitochondrial-disease
#3
REVIEW
James E Davison, Shamima Rahman
Mitochondria are dynamic organelles present in virtually all human cells that are needed for a multitude of cellular functions, including energy production, control of cell apoptosis and numerous biochemical catabolic and synthetic pathways that are critical for cellular health. Primary mitochondrial disorders are a group of greater than 200 single gene defects arising from two genomes (nuclear and mitochondrial) leading to mitochondrial dysfunction, and are associated with extremely heterogeneous phenotypes...
June 24, 2017: Archives of Disease in Childhood
https://www.readbyqxmd.com/read/28647644/from-quantum-measurement-to-biology-via-retrocausality
#4
REVIEW
Koichiro Matsuno
A reaction cycle in general or a metabolic cycle in particular owes its evolutionary emergence to the covering reaction environment acting as a measurement apparatus of a natural origin. The quantum measurement of the environmental origin underlying the molecular processes observed in the biological realm is operative cohesively between the measuring and the measured. The measuring part comes to pull in a quantum as an indivisible lump available from an arbitrary material body to be measured. The inevitable difference between the impinging quantum upon the receiving end on the part of the environment and the actual quantum pulled into the receiving end comes to effectively be nullified through the retrocausative propagation of the corresponding wave function proceeding backwards in time...
June 21, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28647517/proteomics-to-study-macrophage-response-to-viral-infection
#5
Tuula A Nyman, Sampsa Matikainen
Viral infections are a major burden to human and animal health. Immune response against viruses consists of innate and adaptive immunity which are both critical for the eradication of the viral infection. The innate immune system is the first line of defense against viral infections. Proper innate immune response is required for the activation of adaptive, humoral and cell-mediated immunity. Macrophages are innate immune cells which have a central role in detecting viral infections including influenza A and human immunodeficiency viruses...
June 21, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28647498/the-role-of-the-peptides-at-the-origin-of-life
#6
Søren Toxvaerd
The peptides in biosystems are polymers of L-amino acids, but they racemize slowly by an active isomerization kinetics. The chemical reactions in biosystems are, however, reversible and here we show by a thermodynamics analysis and by comprehensive Molecular Dynamics simulations of models of peptides, that the isomerization kinetics racemizes the peptides at high water activity, in agreement with experimental observations of aging of peptides, but enhances homochirality at a smaller water activity. The main conclusion of the simulations is that it is only possible to obtain and maintain homochirality in the presence of a hydrophobic compact core in a peptide of hundreds of chiral units and at a low water activity, and thus the establishment of homochirality at the origin of life and aging of proteins in biosystems might be strongly connected...
June 21, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28646673/quantification-of-evaporation-induced-error-in-atom-probe-tomography-using-molecular-dynamics-simulation
#7
Shu Jian Chen, Xupei Yao, Changxi Zheng, Wen Hui Duan
Non-equilibrium molecular dynamics was used to simulate the dynamics of atoms at the atom probe surface and five objective functions were used to quantify errors. The results suggested that before ionization, thermal vibration and collision caused the atoms to displace up to 1Å and 25Å respectively. The average atom displacements were found to vary between 0.2 and 0.5Å. About 9 to 17% of the atoms were affected by collision. Due to the effects of collision and ion-ion repulsion, the back-calculated positions were on average 0...
June 12, 2017: Ultramicroscopy
https://www.readbyqxmd.com/read/28646471/decoding-early-myelopoiesis-from-dynamics-of-core-endogenous-network
#8
Hang Su, Gaowei Wang, Ruoshi Yuan, Junqiang Wang, Ying Tang, Ping Ao, Xiaomei Zhu
A decade ago mainstream molecular biologists regarded it impossible or biologically ill-motivated to understand the dynamics of complex biological phenomena, such as cancer genesis and progression, from a network perspective. Indeed, there are numerical difficulties even for those who were determined to explore along this direction. Undeterred, seven years ago a group of Chinese scientists started a program aiming to obtain quantitative connections between tumors and network dynamics. Many interesting results have been obtained...
May 29, 2017: Science China. Life Sciences
https://www.readbyqxmd.com/read/28646418/in-vivo-nmr-as-a-tool-for-probing-molecular-structure-and-dynamics-in-intact-chlamydomonas-reinhardtii-cells
#9
Fatemeh Azadi-Chegeni, Christo Schiphorst, Anjali Pandit
We report the application of NMR dynamic spectral editing for probing the structure and dynamics of molecular constituents in fresh, intact cells and in freshly prepared thylakoid membranes of Chlamydomonas reinhardtii (Cr.) green algae. For isotope labeling, wild-type Cr. cells were grown on (13)C acetate-enriched minimal medium. 1D (13)C J-coupling based and dipolar-based MAS NMR spectra were applied to distinguish (13)C resonances of different molecular components. 1D spectra were recorded over a physiological temperature range, and whole-cell spectra were compared to those taken from thylakoid membranes, evaluating their composition and dynamics...
June 23, 2017: Photosynthesis Research
https://www.readbyqxmd.com/read/28646405/revealing-the-importance-of-linkers-in-k-series-oxime-reactivators-for-tabun-inhibited-ache-using-quantum-chemical-docking-and-smd-studies
#10
Shibaji Ghosh, Nellore Bhanu Chandar, Kalyanashis Jana, Bishwajit Ganguly
Inhibition of acetylcholinesterase (AChE) with organophosphorus compounds has a detrimental effect on human life. Oxime K203 seems to be one of the promising reactivators for tabun-inhibited AChE than (K027, K127, and K628). These reactivators differ only in the linker units between the two pyridinium rings. The conformational analyses performed with quantum chemical RHF/6-31G* level for K027, K127, K203 and K628 showed that the minimum energy conformers have different orientations of the active and peripheral pyridinium rings for these reactivator molecules...
June 23, 2017: Journal of Computer-aided Molecular Design
https://www.readbyqxmd.com/read/28646166/atp-release-during-cell-swelling-activates-a-ca-2-dependent-cl-current-by-autocrine-mechanism-in-mouse-hippocampal-microglia
#11
E Murana, F Pagani, B Basilico, M Sundukova, L Batti, S Di Angelantonio, B Cortese, A Grimaldi, A Francioso, P Heppenstall, P Bregestovski, C Limatola, D Ragozzino
Microglia cells, resident immune cells of the brain, survey brain parenchyma by dynamically extending and retracting their processes. Cl(-) channels, activated in the cellular response to stretch/swelling, take part in several functions deeply connected with microglia physiology, including cell shape changes, proliferation, differentiation and migration. However, the molecular identity and functional properties of these Cl(-) channels are largely unknown. We investigated the properties of swelling-activated currents in microglial from acute hippocampal slices of Cx3cr1 (+/GFP) mice by whole-cell patch-clamp and imaging techniques...
June 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28646135/active-translocation-of-a-semiflexible-polymer-assisted-by-an-atp-based-molecular-motor
#12
A Fiasconaro, J J Mazo, F Falo
In this work we study the assisted translocation of a polymer across a membrane nanopore, inside which a molecular motor exerts a force fuelled by the hydrolysis of ATP molecules. In our model the motor switches to its active state for a fixed amount of time, while it waits for an ATP molecule which triggers the motor, during an exponentially distributed time lapse. The polymer is modelled as a beads-springs chain with both excluded volume and bending contributions, and moves in a stochastic three dimensional environment modelled with a Langevin dynamics at a fixed temperature...
June 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28646090/cellular-functions-of-wasp-family-proteins-at-a-glance
#13
REVIEW
Olga Alekhina, Ezra Burstein, Daniel D Billadeau
Proteins of the Wiskott-Aldrich syndrome protein (WASP) family function as nucleation-promoting factors for the ubiquitously expressed Arp2/3 complex, which drives the generation of branched actin filaments. Arp2/3-generated actin regulates diverse cellular processes, including the formation of lamellipodia and filopodia, endocytosis and/or phagocytosis at the plasma membrane, and the generation of cargo-laden vesicles from organelles including the Golgi, endoplasmic reticulum (ER) and the endo-lysosomal network...
June 23, 2017: Journal of Cell Science
https://www.readbyqxmd.com/read/28645943/the-structure-of-the-tetanus-toxin-reveals-ph-mediated-domain-dynamics
#14
Geoffrey Masuyer, Julian Conrad, Pål Stenmark
The tetanus neurotoxin (TeNT) is a highly potent toxin produced by Clostridium tetani that inhibits neurotransmission of inhibitory interneurons, causing spastic paralysis in the tetanus disease. TeNT differs from the other clostridial neurotoxins by its unique ability to target the central nervous system by retrograde axonal transport. The crystal structure of the tetanus toxin reveals a "closed" domain arrangement stabilised by two disulphide bridges, and the molecular details of the toxin's interaction with its polysaccharide receptor...
June 23, 2017: EMBO Reports
https://www.readbyqxmd.com/read/28645833/binding-kinetics-and-pathways-of-ligands-to-gpcrs
#15
REVIEW
Andrea Strasser, Hans-Joachim Wittmann, Roland Seifert
Previously, drugs were developed focusing on target affinity and selectivity. However, it is becoming evident that the drug-target residence time, related to the off-rate, is an important parameter for successful drug development. The residence time influences both the on-rate and overall effectiveness of drugs. Furthermore, ligand binding is now appreciated to be a multistep process because metastable and/or intermediate binding sites in the extracellular region have been identified. In this review, we summarize experimental ligand-binding data for G-protein-coupled receptors (GPCRs), and their binding pathways, analyzed by molecular dynamics (MD)...
June 20, 2017: Trends in Pharmacological Sciences
https://www.readbyqxmd.com/read/28645570/quantitative-proteomics-analysis-by-itraq-revealed-underlying-changes-in-thermotolerance-of-arthrospira-platensis
#16
Rong Chang, Bingxin Lv, Bosheng Li
Growth temperature is a critical factor that affects cultivation of Arthrospira platensis which is a type of cyanobacterium widely known as Spirulina that has significant commercial value. To investigate the molecular mechanism underlying the thermotolerance of Spirulina, differential protein expression profiling was carried out using iTRAQ-based quantitative proteomic analysis. This study only analyzed changes in thylakoids. Among the 2085 proteins quantified, 43 differentially expressed proteins were selected based on the fold change cutoff scores of ≥2 or ≤0...
June 20, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28645245/transcriptomic-dynamics-in-soybean-near-isogenic-lines-differing-in-alleles-for-an-aphid-resistance-gene-following-infestation-by-soybean-aphid-biotype-2
#17
Sungwoo Lee, Bryan J Cassone, Asela Wijeratne, Tae-Hwan Jun, Andrew P Michel, M A Rouf Mian
BACKGROUND: Genetic resistance of soybean [Glycine max (L.) Merr] against Aphis glycines provides effective management of this invasive pest, though the underlying molecular mechanisms are largely unknown. This study aimed to investigate genome-wide changes in gene expressions of soybean near-isogenic lines (NILs) either with the Rag5 allele for resistance or the rag5 allele for susceptibility to the aphid following infestation with soybean aphid biotype 2. RESULTS: The resistant (R)-NIL responded more rapidly to aphid infestation than the susceptible (S)-NIL, with differential expressions of 2496 genes during first 12 h of infestation (hai), compared to the aphid-free control...
June 23, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28645195/mutational-biases-influence-parallel-adaptation
#18
Arlin Stoltzfus, David M McCandlish
While mutational biases strongly influence neutral molecular evolution, the role of mutational biases in shaping the course of adaptation is less clear. Here we consider the frequency of transitions relative to transversions among adaptive substitutions. Because mutation rates for transitions are higher than those for transversions, if mutational biases influence the dynamics of adaptation, then transitions should be over-represented among documented adaptive substitutions. To test this hypothesis, we assembled 2 sets of data on putatively adaptive amino acid replacements that have occurred in parallel during evolution, either in nature or in the laboratory...
June 22, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28645155/features-of-genomic-organization-in-a-nucleotide-resolution-molecular-model-of-the-escherichia-coli-chromosome
#19
William C Hacker, Shuxiang Li, Adrian H Elcock
We describe structural models of the Escherichia coli chromosome in which the positions of all 4.6 million nucleotides of each DNA strand are resolved. Models consistent with two basic chromosomal orientations, differing in their positioning of the origin of replication, have been constructed. In both types of model, the chromosome is partitioned into plectoneme-abundant and plectoneme-free regions, with plectoneme lengths and branching patterns matching experimental distributions, and with spatial distributions of highly-transcribed chromosomal regions matching recent experimental measurements of the distribution of RNA polymerases...
June 22, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28645089/drug-resistance-mechanism-of-l10f-l10f-n88s-and-l90m-mutations-in-crf01_ae-hiv-1-protease-molecular-dynamics-simulations-and-binding-free-energy-calculations
#20
C S Vasavi, Ramasamy Tamizhselvi, Punnagai Munusami
HIV-1 protease plays a crucial role in viral replication and maturation, which makes it one of the most attractive targets for anti-retroviral therapy. The majority of HIV infections in developing countries are due to non-B subtype. Subtype AE is spreading rapidly and infecting huge population worldwide. The mutations in the active site of subtype AE directly impair the interactions with the inhibitor. The non-active site mutations influence the binding of the inhibitor indirectly and their resistance mechanism is not well understood...
June 8, 2017: Journal of Molecular Graphics & Modelling
keyword
keyword
24561
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"