keyword
MENU ▼
Read by QxMD icon Read
search

Protein dynamic

keyword
https://www.readbyqxmd.com/read/28531815/chicken-interleukin-1%C3%AE-mutants-are-effective-single-dose-vaccine-adjuvants-that-enhance-mucosal-immune-response
#1
Wen-Ting Chen, Hao-Kai Chang, Cheng-Chung Lin, Shan-Min Yang, Hsien-Sheng Yin
The use of cytokines as adjuvants in poultry is promising because they may enhance immune responses to antigens. In this study, we created two mutants, chicken interleukin-1 beta (ChIL-1β) Q19A and R140A, which exhibited significantly increased in vivo biological activity compared with wild-type ChIL-1β. The potential mucosal adjuvant activity of the mutants Q19A and R140A was evaluated in chickens through the intranasal coadministration of a single dose of the Newcastle disease virus (NDV) vaccine with Q19A or R140A...
May 19, 2017: Molecular Immunology
https://www.readbyqxmd.com/read/28531373/identification-of-potential-inhibitors-for-hcv-ns3-genotype-4a-by-combining-protein-ligand-interaction-fingerprint-3d-pharmacophore-docking-and-dynamic-simulation
#2
Mahmoud Abd El-Monem El-Hasab, Eman Esmat El-Bastawissy, Tarek Faathy El-Moselhy
HCV NS3 protease domain has been one of the most attractive targets for developing new drugs for HCV infection and many drugs were successfully developed, but all of them were designed for targeting HCV genotype 1 infection. HCV genotype 4a dominant in Egypt has paid less attention. Here we describe our protocol of virtual screening in identification of novel potential potent inhibitors for HCV NS3 of genotype 4a using homology modelling, PLIF (protein ligand interaction fingerprint), docking, pharmacophore and dynamic simulation...
May 20, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28531371/wing-1-of-protein-hop2-is-as-important-as-helix-3-in-dna-binding-by-md-simulation
#3
Hem Moktan, Donghua H Zhou
The repair of programmed DNA double-strand breaks through recombination is required for proper association and disjunction of the meiotic homologous chromosomes. Meiosis specific protein HOP2 plays essential roles in recombination by promoting recombinase activities. The N-terminal domain of HOP2 interacts with DNA through helix 3 (H3) and wing 1 (W1). Mutations in wing 1 (Y65A/K67A/Q68A) slightly weakened the binding but mutations in helices 2 and 3 (Q30A/K44A/K49A) nearly abolished the binding. To better understand such differential effects at atomic level, molecular dynamics simulations were employed...
May 20, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28531352/conformational-complexity-in-the-lh2-antenna-of-the-purple-sulfur-bacterium-allochromatium-vinosum-revealed-by-hole-burning-spectroscopy
#4
Adam Kell, Mahboobe Jassas, Khem Acharya, Kirsty Hacking, Richard J Cogdell, Ryszard J Jankowiak
This work discusses the protein conformational complexity of the B800-850 LH2 complexes from the purple sulfur bacterium Allochromatium vinosum, focusing on the spectral characteristics of the B850 chromophores. Low-temperature B850 absorption and the split B800 band shift blue and red, respectively, at elevated temperatures, revealing isosbestic points. The latter indicates the presence of two (unresolved) conformations of B850 bacteriochlorophylls (BChls), referred to as conformations 1 and 2, and two conformations of B800 BChls, denoted as B800R and B800B...
May 22, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28531272/a-novel-isoform-of-tet1-that-lacks-a-cxxc-domain-is-overexpressed-in-cancer
#5
Charly R Good, Jozef Madzo, Bela Patel, Shinji Maegawa, Nora Engel, Jaroslav Jelinek, Jean-Pierre J Issa
TET1 oxidizes methylated cytosine into 5-hydroxymethylcytosine (5hmC), resulting in regulation of DNA methylation and gene expression. Full length TET1 (TET1FL) has a CXXC domain that binds to unmethylated CpG islands (CGIs). This CXXC domain allows TET1 to protect CGIs from aberrant methylation, but it also limits its ability to regulate genes outside of CGIs. Here, we report a novel isoform of TET1 (TET1ALT) that has a unique transcription start site from an alternate promoter in intron 2, yielding a protein with a unique translation start site...
May 22, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28531263/in-vivo-dynamics-of-the-cortical-actin-network-revealed-by-fast-scanning-atomic-force-microscopy
#6
Yanshu Zhang, Aiko Yoshida, Nobuaki Sakai, Yoshitsugu Uekusa, Masahiro Kumeta, Shige H Yoshimura
Together with lamellipodia and stress fibers, a dynamic network of actin filaments in the cell cortex plays a major role in the maintenance of cell morphology and motility. In contrast to lamellipodia, which have been well studied in various motile cells, the dynamics of actin filaments in the cell cortex have not yet been clarified due to a lack of proper imaging techniques. Here, we utilized high-speed atomic force microscopy for live-cell imaging and analyzed cortical actin dynamics in living cells. We successfully measured the polymerization rate and the frequency of filament synthesis in living COS-7 cells, and examined the associated effects of various inhibitors and actin-binding proteins...
May 20, 2017: Microscopy
https://www.readbyqxmd.com/read/28531251/ca2-dependent-phosphoregulation-of-the-plasma-membrane-ca2-atpase-aca8-modulates-stimulus-induced-calcium-signatures
#7
Alex Costa, Laura Luoni, Claudia Adriana Marrano, Kenji Hashimoto, Philipp Köster, Sonia Giacometti, Maria Ida De Michelis, Jörg Kudla, Maria Cristina Bonza
Ca2+ signals are transient, hence, upon a stimulus-induced increase in cytosolic Ca2+ concentration, cells have to re-establish resting Ca2+ levels. Ca2+ extrusion is operated by a wealth of transporters, such as Ca2+ pumps and Ca2+/H+ antiporters, which often require a rise in Ca2+ concentration to be activated. Here, we report a regulatory fine-tuning mechanism of the Arabidopsis thaliana plasma membrane-localized Ca2+-ATPase isoform ACA8 that is mediated by calcineurin B-like protein (CBL) and CBL-interacting protein kinase (CIPK) complexes...
May 20, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28531234/directed-evolution-to-improve-the-catalytic-efficiency-of-urate-oxidase-from-bacillus-subtilis
#8
Wenjie Li, Shouteng Xu, Biao Zhang, Yelin Zhu, Yan Hua, Xin Kong, Lianhong Sun, Jiong Hong
Urate oxidase is a key enzyme in purine metabolism and catalyzes the oxidation of uric acid to allantoin. It is used to treat hyperuricemia and gout, and also in a diagnostic kit. In this study, error-prone polymerase chain reaction and staggered extension process was used to generate a mutant urate oxidase with improved enzyme activity from Bacillus subtilis. After several rounds of mutagenesis and screening, two mutants 6E9 and 8E279 were obtained which exhibited 2.99 and 3.43 times higher catalytic efficiency, respectively...
2017: PloS One
https://www.readbyqxmd.com/read/28530826/high-speed-atomic-force-microscopy-reveals-loss-of-nuclear-pore-resilience-as-a-dying-code-in-colorectal-cancer-cells
#9
Mahmoud Shaaban Mohamed, Akiko Kobayashi, Azuma Taoka, Takahiro Watanabe-Nakayama, Yosuke Kikuchi, Masaharu Hazawa, Toshinari Minamoto, Yoshihiro Fukumori, Noriyuki Kodera, Takayuki Uchihashi, Toshio Ando, Richard W Wong
Nuclear pore complexes (NPCs) are the sole turnstile implanted in the nuclear envelope (NE), acting as a central nano-regulator of transport between the cytosol and the nucleus. NPCs consist of ~30 proteins, termed nucleoporins. About one-third of nucleoporins harbour natively unstructured, intrinsically disordered phenylalanine-glycine strings (FG-Nups), which engage in transport selectivity. Because the barriers insert deeply in the NPC, they are nearly inaccessible. Several in vitro barrier models have been proposed; however, the dynamic FG-Nups protein molecules themselves are imperceptible in vivo...
May 22, 2017: ACS Nano
https://www.readbyqxmd.com/read/28530823/nanomechanically-visualizing-drug-cell-interaction-at-the-early-stage-of-chemotherapy
#10
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/28530812/probing-the-binding-modes-of-a-multi-domain-protein-to-lipid-based-nanoparticles-by-relaxation-based-nmr
#11
Alberto Ceccon, Vitali Tugarinov, Andrew J Boughton, David Fushman, G Marius Clore
The interactions of two model multi-domain proteins - covalently linked di-ubiquitins, Ub2 - with lipid-based nanoparticles have been quantitatively probed by the measurements of NMR lifetime line broadening, ΔR2. By combined analysis of ΔR2 profiles arising from interactions with liposomes of varying sizes, an approach recently developed for the characterization of interactions of mono-ubiquitin with liposomes, we determine how the parameters of exchange (liposome binding) and dynamics of each individual domain of Ub2 on the surface of liposomes change when the domains are covalently attached to one another by a flexible linker...
May 22, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28530795/modelling-living-cells-response-to-surface-tension-and-chemical-patterns
#12
Marco Macis, Francesca Lugli, Francesco Zerbetto
Mechanobiology is an important epigenetic factor. It influences cell functioning and bears on gene induction, protein synthesis, cell growth and differentiation. In the presence of patterned chemical cues, living cells can take shapes that are far from that of a drop of fluid. These shapes are characterized by inward curvatures that are pinned at the points of location of the cues. The mechano-chemical interactions that orchestrate cell behavior is simulated and controlled by modeling the cells as made by parcels of fluid...
May 22, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28530650/multi-virion-infectious-units-arise-from-free-viral-particles-in-an-enveloped-virus
#13
José M Cuevas, María Durán-Moreno, Rafael Sanjuán
Many animal viruses are enveloped in a lipid bilayer taken up from cellular membranes. Because viral surface proteins bind to these membranes to initiate infection, we hypothesized that free virions may also be capable of interacting with the envelopes of other virions extracellularly. Here, we demonstrate this hypothesis in the vesicular stomatitis virus (VSV), a prototypic negative-strand RNA virus composed of an internal ribonucleocapsid, a matrix protein and an external envelope(1). Using microscopy, dynamic light scattering, differential centrifugation and flow cytometry, we show that free viral particles can spontaneously aggregate into multi-virion infectious units...
May 22, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28530285/one-step-formulation-of-nonionic-surfactant-bicelles-nsbs-by-a-double-tailed-polyglycerol-type-nonionic-surfactant
#14
Kenji Aramaki, Chikahiro Iwata, Jitendra Mata, Tetsuya Maehara, Daisuke Aburano, Yuichi Sakanishi, Kyuhei Kitao
Bicelles are generally formed by phospholipid-based systems and are useful for various applications, such as nanocarriers or membrane protein crystallization. The same disc-like assemblies, nonionic surfactant bicelles (NSBs), can also be formed using nonionic amphiphiles, but this has not been reported extensively. We report a novel NSB system that employs the double-tailed nonionic amphiphile, polyglyceryl dialkyl ether (C12CmGn), which has two alkyl chains and a polyglyceryl group. A symmetric-tail molecule, C12C12G13...
May 22, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28530269/a-critical-comparison-of-coarse-grained-structure-based-approaches-and-atomic-models-of-protein-folding
#15
Jie Hu, Tao Chen, Moye Wang, Hue Sun Chan, Zhuqing Zhang
Structure-based coarse-grained Gō-like models have been used extensively in deciphering protein folding mechanisms because of their simplicity and tractability. Meanwhile, explicit-solvent molecular dynamics (MD) simulations with physics-based all-atom force fields have been applied successfully to simulate folding/unfolding transitions for several small, fast-folding proteins. To explore the degree to which coarse-grained Gō-like models and their extensions to incorporate nonnative interactions are capable of producing folding processes similar to those in all-atom MD simulations, here we systematically compare the computed unfolded states, transition states, and transition paths obtained using coarse-grained models and all-atom explicit-solvent MD simulations...
May 22, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28529975/phylogenetic-analyses-suggest-that-factors-other-than-the-capsid-protein-play-a-role-in-the-epidemic-potential-of-gii-2-norovirus
#16
Kentaro Tohma, Cara J Lepore, Lauren A Ford-Siltz, Gabriel I Parra
Norovirus is the leading cause of acute gastroenteritis worldwide. For over two decades, a single genotype (GII.4) has been responsible for most norovirus-associated cases. However, during the winter of 2014 to 2015, the GII.4 strains were displaced by a rarely detected genotype (GII.17) in several countries of the Asian continent. Moreover, during the winter of 2016 to 2017, the GII.2 strain reemerged as predominant in different countries worldwide. This reemerging GII.2 strain is a recombinant virus that presents a GII...
May 2017: MSphere
https://www.readbyqxmd.com/read/28529725/the-catalytic-function-of-cytochrome-p450-is-entwined-with-its-membrane-bound-nature
#17
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/28529698/seven-perspectives-on-gpcr-h-d-exchange-proteomics-methods
#18
Xi Zhang
Recent research shows surging interest to visualize human G protein-coupled receptor (GPCR) dynamic structures using the bottom-up H/D-exchange (HDX) proteomics technology. This opinion article clarifies critical technical nuances and logical thinking behind the GPCR HDX proteomics method, to help scientists overcome cross-discipline pitfalls, and understand and reproduce the protocol at high quality. The 2010 89% HDX structural coverage of GPCR was achieved with both structural and analytical rigor. This article emphasizes systematically considering membrane protein structure stability and compatibility with chromatography and mass spectrometry (MS) throughout the pipeline, including the effects of metal ions, zero-detergent shock, and freeze-thaws on HDX result rigor...
2017: F1000Research
https://www.readbyqxmd.com/read/28529592/unique-insight-into-microenvironmental-changes-in-colorectal-cancer-ex-vivo-assessment-of-matrix-metalloprotease-mediated-molecular-changes-in-human-colorectal-tumor-tissue-and-corresponding-non-neoplastic-adjacent-tissue
#19
Nicholas Willumsen, Cecilie L Bager, Anne-Christine Bay-Jensen, Stephanie N Kehlet, Henrik Harling, Diana J Leeming, Morten A Karsdal, Lars N Jorgensen
Matrix metalloprotease (MMP)-mediated tissue remodeling is one of the malignant changes driving colorectal cancer. Measurement of altered MMP expression/activity is not sufficient to fully understand the effect of MMP-mediated tissue remodeling. Biomarkers are required that specifically reflect the dynamic processes of the MMP-mediated degradation of signature proteins from colorectal tissue. The aim of the present study was to profile and characterize the release of MMP-degraded type III collagen (C3M) and citrullinated and MMP-degraded vimentin (VICM) from tumor tissue and corresponding non-neoplastic adjacent tissue (NAT) in a human colorectal cancer ex vivo model...
May 2017: Oncology Letters
https://www.readbyqxmd.com/read/28529520/katanin-1-is-essential-for-embryogenesis-and-seed-formation-in-arabidopsis
#20
Ivan Luptovčiak, Despina Samakovli, George Komis, Jozef Šamaj
Cytoskeletal remodeling has a fundamental role, especially during transitional developmental stages when cells rapidly adopt new forms and roles, like gametogenesis, fertilization and concomitant embryogenesis and seed formation. KATANIN 1, a microtubule severing protein, fulfills a major regulatory mechanism of dynamic microtubule turnover in eukaryotes. Herein, we show that three well-established KATANIN 1 mutants, fra2, lue1 and ktn1-2 collectively display lower fertility and seed set in Arabidopsis. These lower fertility and seed set rates of fra2, lue1 and ktn1-2 mutants were correlated to abnormalities in the development of embryo proper and seed...
2017: Frontiers in Plant Science
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"