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Protein dynamic

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https://www.readbyqxmd.com/read/27914080/immobilization-techniques-of-bacteria-for-live-super-resolution-imaging-using-structured-illumination-microscopy
#1
Amy L Bottomley, Lynne Turnbull, Cynthia B Whitchurch, Elizabeth J Harry
Advancements in optical microscopy technology have allowed huge progression in the ability to understand protein structure and dynamics in live bacterial cells using fluorescence microscopy. Paramount to high-quality microscopy is good sample preparation to avoid bacterial cell movement that can result in motion blur during image acquisition. Here, we describe two techniques of sample preparation that reduce unwanted cell movement and are suitable for application to a number of bacterial species and imaging methods...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914070/analysis-of-bacterial-surface-interactions-with-mass-spectrometry-based-proteomics
#2
Christofer Karlsson, Johan Teleman, Johan Malmström
Host-pathogen protein-protein interaction networks are highly complex and dynamic. In this experimental protocol we describe a method to isolate host proteins attached to the bacterial surface followed by quantitative mass spectrometry based proteomics analysis. This technique provides an overview of the host-pathogen interaction network, which can be used to guide directed perturbations of the system, and to select target of specific interest for further studies.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914065/computational-design-of-membrane-curvature-sensing-peptides
#3
Armando Jerome de Jesus, Hang Yin
Computer simulations have become an indispensable tool in studying molecular biological systems. The unmatched spatial and temporal resolution that it offers enables for microscopic-level views into the dynamics and mechanics of biological systems. Recent advances in hardware resources have also opened up to computer simulations the investigation of longer timescale biological processes and larger systems. The study of membrane proteins or peptides especially benefits from simulations due to difficulties related to crystallization of such proteins in a membrane environment...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914052/applications-of-normal-mode-analysis-methods-in-computational-protein-design
#4
Vincent Frappier, Matthieu Chartier, Rafael Najmanovich
Recent advances in coarse-grained normal mode analysis methods make possible the large-scale prediction of the effect of mutations on protein stability and dynamics as well as the generation of biologically relevant conformational ensembles. Given the interplay between flexibility and enzymatic activity, the combined analysis of stability and dynamics using the Elastic Network Contact Model (ENCoM) method has ample applications in protein engineering in industrial and medical applications such as in computational antibody design...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914051/integration-of-molecular-dynamics-based-predictions-into-the-optimization-of-de-novo-protein-designs-limitations-and-benefits
#5
Henrique F Carvalho, Arménio J M Barbosa, Ana C A Roque, Olga Iranzo, Ricardo J F Branco
Recent advances in de novo protein design have gained considerable insight from the intrinsic dynamics of proteins, based on the integration of molecular dynamics simulations protocols on the state-of-the-art de novo protein design protocols used nowadays. With this protocol we illustrate how to set up and run a molecular dynamics simulation followed by a functional protein dynamics analysis. New users will be introduced to some useful open-source computational tools, including the GROMACS molecular dynamics simulation software package and ProDy for protein structural dynamics analysis...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914045/achievements-and-challenges-in-computational-protein-design
#6
Ilan Samish
Computational protein design (CPD), a yet evolving field, includes computer-aided engineering for partial or full de novo designs of proteins of interest. Designs are defined by a requested structure, function, or working environment. This chapter describes the birth and maturation of the field by presenting 101 CPD examples in a chronological order emphasizing achievements and pending challenges. Integrating these aspects presents the plethora of CPD approaches with the hope of providing a "CPD 101". These reflect on the broader structural bioinformatics and computational biophysics field and include: (1) integration of knowledge-based and energy-based methods, (2) hierarchical designated approach towards local, regional, and global motifs and the integration of high- and low-resolution design schemes that fit each such region, (3) systematic differential approaches towards different protein regions, (4) identification of key hot-spot residues and the relative effect of remote regions, (5) assessment of shape-complementarity, electrostatics and solvation effects, (6) integration of thermal plasticity and functional dynamics, (7) negative design, (8) systematic integration of experimental approaches, (9) objective cross-assessment of methods, and (10) successful ranking of potential designs...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27913905/proteins-immunologically-related-to-map65-1-accumulate-and-localize-differentially-during-bud-development-in-vitis-vinifera-l
#7
Luigi Parrotta, Claudia Faleri, Mauro Cresti, Giampiero Cai
Various arrays of microtubules are present throughout the plant cell cycle and are involved in distinct functions. Microtubule-associated proteins (MAPs) regulate microtubule dynamics by acting as stabilizers, destabilizers, and promoters of microtubule dynamics. The MAP65 family is a specific group of cross-linkers required for structural maintenance of microtubules. In plants, different isoforms of MAP65 are differentially expressed according to their developmental program. In this work, we analyzed the differential distribution of proteins immunologically related to MAP65-1 during bud development in grapevine (Vitis vinifera L...
December 2, 2016: Protoplasma
https://www.readbyqxmd.com/read/27913887/transcriptomics-analysis-of-hulless-barley-during-grain-development-with-a-focus-on-starch-biosynthesis
#8
Yawei Tang, Xingquan Zeng, Yulin Wang, Lijun Bai, Qijun Xu, Zexiu Wei, Hongjun Yuan, Tashi Nyima
Hulless barley, with its unique nutritional value and potential health benefits, has increasingly attracted attentions in recent years. However, the transcription dynamics during hulless barley grain development is not well understood. In the present study, we investigated the transcriptome changes during barley grain development using Illumina paired-end RNA-sequencing. Two datasets of the developing grain transcriptomes from two barley landraces with the differential seed starch synthesis traits were generated, and comparative transcriptome approach in both genotypes was performed...
December 2, 2016: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/27913731/disentangling-polydispersity-in-the-pcna-p15paf-complex-a-disordered-transient-and-multivalent-macromolecular-assembly
#9
Tiago N Cordeiro, Po-Chia Chen, Alfredo De Biasio, Nathalie Sibille, Francisco J Blanco, Jochen S Hub, Ramon Crehuet, Pau Bernadó
The intrinsically disordered p15(PAF) regulates DNA replication and repair when interacting with the Proliferating Cell Nuclear Antigen (PCNA) sliding clamp. As many interactions between disordered proteins and globular partners involved in signaling and regulation, the complex between p15(PAF) and trimeric PCNA is of low affinity, forming a transient complex that is difficult to characterize at a structural level due to its inherent polydispersity. We have determined the structure, conformational fluctuations, and relative population of the five species that coexist in solution by combining small-angle X-ray scattering (SAXS) with molecular modelling...
December 1, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27913680/new-nuclear-and-perinuclear-functions-of-formins
#10
REVIEW
Tadamoto Isogai, Metello Innocenti
Formin family proteins (formins) represent an evolutionary conserved protein family encoded in the genome of a wide range of eukaryotes. Formins are hallmarked by a formin homology 1 (FH1) domain juxtaposed to an FH2 domain whereby they control actin and microtubule dynamics. Not surprisingly, formins are best known as key regulators of the cytoskeleton in a variety of morphogenetic processes. However, mounting evidence implicates several formins in the assembly and organization of actin within and around the nucleus...
December 15, 2016: Biochemical Society Transactions
https://www.readbyqxmd.com/read/27913204/the-selective-bcl-2-inhibitor-venetoclax-a-bh3-mimetic-does-not-dysregulate-intracellular-ca-2-signaling
#11
Tamara Vervloessem, Hristina Ivanova, Tomas Luyten, Jan B Parys, Geert Bultynck
Anti-apoptotic B cell-lymphoma-2 (Bcl-2) proteins are emerging as therapeutic targets in a variety of cancers for precision medicines, like the BH3-mimetic drug venetoclax (ABT-199), which antagonizes the hydrophobic cleft of Bcl-2. However, the impact of venetoclax on intracellular Ca(2+) homeostasis and dynamics in cell systems has not been characterized in detail. Here, we show that venetoclax did not affect Ca(2+)-transport systems from the endoplasmic reticulum (ER) in permeabilized cell systems. Venetoclax (1μM) did neither trigger Ca(2+) release by itself nor affect agonist-induced Ca(2+) release in a variety of intact cell models...
November 29, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27913116/multiple-conformations-of-gal3-protein-drive-the-galactose-induced-allosteric-activation-of-the-gal-genetic-switch-of-saccharomyces-cerevisiae
#12
Rajesh Kumar Kar, Hungyo Kharerin, Ranjith Padinhateeri, Paike Jayadeva Bhat
Gal3p is an allosteric monomeric protein which activates the GAL genetic switch of Saccharomyces cerevisiae in response to galactose. Expression of constitutive mutant of Gal3p or overexpression of wild-type Gal3p activates the GAL switch in the absence of galactose. These data suggest that Gal3p exists as an ensemble of active and inactive conformations. Structural data has indicated that Gal3p exists in open (inactive) and closed (active) conformations. However, mutant of Gal3p that predominantly exists in inactive conformation and yet capable of responding to galactose has not been isolated...
November 29, 2016: Journal of Molecular Biology
https://www.readbyqxmd.com/read/27912878/selecting-optimum-protein-nano-carriers-for-natural-polyphenols-using-chemoinformatics-tools
#13
AbdelKader A Metwally, Sherweit H El-Ahmady, Rania M Hathout
BACKGROUND: The normal fate of any natural product with a therapeutic potential is to be formulated into an effective medicine. However, the conventional methods of selecting the suitable formulations or carriers based on the formulator experiences, trials and errors as well as materials availability do not usually yield the optimal results. HYPOTHESIS: We hypothesize the possibility of the virtual optimum selection of a protein carrier for two polyphenolic compounds widely investigated for their chemopreventive effects; resveratrol and curcumin using a combination of some chemoinformatics tools...
December 15, 2016: Phytomedicine: International Journal of Phytotherapy and Phytopharmacology
https://www.readbyqxmd.com/read/27912844/heparanase-from-basic-research-to-therapeutic-applications-in-cancer-and-inflammation
#14
Israel Vlodavsky, Preeti Singh, Ilanit Boyango, Lilach Gutter-Kapon, Michael Elkin, Ralph D Sanderson, Neta Ilan
Heparanase, the sole heparan sulfate degrading endoglycosidase, regulates multiple biological activities that enhance tumor growth, angiogenesis and metastasis. Heparanase expression is enhanced in almost all cancers examined including various carcinomas, sarcomas and hematological malignancies. Numerous clinical association studies have consistently demonstrated that upregulation of heparanase expression correlates with increased tumor size, tumor angiogenesis, enhanced metastasis and poor prognosis. In contrast, knockdown of heparanase or treatments of tumor-bearing mice with heparanase-inhibiting compounds, markedly attenuate tumor progression further underscoring the potential of anti-heparanase therapy for multiple types of cancer...
November 2016: Drug Resistance Updates: Reviews and Commentaries in Antimicrobial and Anticancer Chemotherapy
https://www.readbyqxmd.com/read/27912243/vomeronasal-receptors-in-vertebrates-and-the-evolution-of-pheromone-detection
#15
Liliana Silva, Agostinho Antunes
Pheromones were identified as chemical signals used for intraspecific communication in insects (e.g., sexual attraction) in the 1950s. However, only almost 40 years later the vomeronasal receptors type-1 (V1R) and type-2 (V2R) were identified, usually associated with the presence of a vomeronasal organ (VNO). VRs are widespread in amphibians, reptiles, and mammals, but birds lost the VNO. Similarly, fishes lack VRs and a VNO but can still detect pheromones, instead using the olfactory receptors related to class A and class C G protein-coupled receptors...
November 28, 2016: Annual Review of Animal Biosciences
https://www.readbyqxmd.com/read/27912143/coupling-of-helix-e-f-motion-with-the-o-nitrito-and-2-nitrovinyl-coordination-in-myoglobin
#16
Androulla Ioannou, Alexandra Lambrou, Vangelis Daskalakis, Eftychia Pinakoulaki
Myoglobin (Mb) is known to react slowly with nitirite to form the green pigment by NO2(-) cordination to the heme Fe in the O-binding nitrito (O1NO2) mode and to the heme 2-vinyl position. Nitrite is a powerful oxidizing agent and a biological reservoir for NO that has been implicated in a variety of aerobic biological systems. Accordingly, it is important to elucidate the nature and variety of NO2(-) reaction mechanisms with Mb. We have performed principal component analysis (PCA, or essential dynamics) on Molecular Dynamics trajectories of all MbNO2 coordination states to resolve the most important motions in the protein at 298K...
November 25, 2016: Biophysical Chemistry
https://www.readbyqxmd.com/read/27912064/modular-assembly-of-the-bacterial-large-ribosomal-subunit
#17
Joseph H Davis, Yong Zi Tan, Bridget Carragher, Clinton S Potter, Dmitry Lyumkis, James R Williamson
The ribosome is a complex macromolecular machine and serves as an ideal system for understanding biological macromolecular assembly. Direct observation of ribosome assembly in vivo is difficult, as few intermediates have been isolated and thoroughly characterized. Herein, we deploy a genetic system to starve cells of an essential ribosomal protein, which results in the accumulation of assembly intermediates that are competent for maturation. Quantitative mass spectrometry and single-particle cryo-electron microscopy reveal 13 distinct intermediates, which were each resolved to ∼4-5 Å resolution and could be placed in an assembly pathway...
December 1, 2016: Cell
https://www.readbyqxmd.com/read/27911875/autophagy-flux-induced-by-ginsenoside-rg3-attenuates-human-prion-protein-mediated-neurotoxicity-and-mitochondrial-dysfunction
#18
Ji-Hong Moon, Ju-Hee Lee, You-Jin Lee, Sang-Youel Park
Mitochondrial quality control is a process by which mitochondria undergo successive rounds of fusion and fission with dynamic exchange of components to segregate functional and damaged elements. Removal of mitochondrion that contains damaged components is accomplished via autophagy. In this study, we investigated whether ginsenoside Rg3, an active ingredient of the herbal medicine ginseng that is used as a tonic and restorative agent, could attenuate prion peptide, PrP (106-126)-induced neurotoxicity and mitochondrial damage...
November 30, 2016: Oncotarget
https://www.readbyqxmd.com/read/27911818/planar-cell-polarity-signaling-in-the-uterus-directs-appropriate-positioning-of-the-crypt-for-embryo-implantation
#19
Jia Yuan, Jeeyeon Cha, Wenbo Deng, Amanda Bartos, Xiaofei Sun, Hsin-Yi Henry Ho, Jean-Paul Borg, Terry P Yamaguchi, Yingzi Yang, Sudhansu K Dey
Blastocyst implantation is a complex process requiring coordination of a dynamic sequence of embryo-uterine interactions. Blood vessels enter the uterus from the mesometrium, demarcating the uterus into mesometrial (M) and antimesometrial (AM) domains. Implantation occurs along the uterine longitudinal axis within specialized implantation chambers (crypts) that originate within the evaginations directed from the primary lumen toward the AM domain. The morphological orientation of crypts in rodent uteri was recognized more than a century ago, but the mechanism remained unknown...
November 28, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27911811/the-structure-of-the-catechin-binding-site-of-human-sulfotransferase-1a1
#20
Ian Cook, Ting Wang, Mark Girvin, Thomas S Leyh
We are just beginning to understand the allosteric regulation of the human cytosolic sulfotransferase (SULTs) family-13 disease-relevant enzymes that regulate the activities of hundreds, if not thousands, of signaling small molecules. SULT1A1, the predominant isoform in adult liver, harbors two noninteracting allosteric sites, each of which binds a different molecular family: the catechins (naturally occurring flavonols) and nonsteroidal antiinflammatory drugs (NSAIDs). Here, we present the structure of an SULT allosteric binding site-the catechin-binding site of SULT1A1 bound to epigallocatechin gallate (EGCG)...
November 23, 2016: Proceedings of the National Academy of Sciences of the United States of America
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