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Protein dynamic

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https://www.readbyqxmd.com/read/28346455/collective-helicity-switching-of-a-dna-coat-assembly
#1
Yongju Kim, Huichang Li, Ying He, Xi Chen, Xiaoteng Ma, Myongsoo Lee
Hierarchical assemblies of biomolecular subunits can carry out versatile tasks at the cellular level with remarkable spatial and temporal precision. As an example, the collective motion and mutual cooperation between complex protein machines mediate essential functions for life, such as replication, synthesis, degradation, repair and transport. Nucleic acid molecules are far less dynamic than proteins and need to bind to specific proteins to form hierarchical structures. The simplest example of these nucleic acid-based structures is provided by a rod-shaped tobacco mosaic virus, which consists of genetic material surrounded by coat proteins...
March 27, 2017: Nature Nanotechnology
https://www.readbyqxmd.com/read/28346426/mrl-proteins-cooperate-with-activated-ras-in-glia-to-drive-distinct-oncogenic-outcomes
#2
E Taylor, N Alqadri, L Dodgson, D Mason, E Lyulcheva, G Messina, D Bennett
The Mig10/RIAM/Lpd (MRL) adapter protein Lpd regulates actin dynamics through interactions with Scar/WAVE and Ena/VASP proteins to promote the formation of cellular protrusions and to stimulate invasive migration. However, the ability of MRL proteins to interact with multiple actin regulators and to promote serum response factor (SRF) signalling has raised the question of whether MRL proteins employ alternative downstream mechanisms to drive oncogenic processes in a context-dependent manner. Here, using a Drosophila model, we show that overexpression of either human Lpd or its Drosophila orthologue Pico can promote growth and invasion of Ras(V12)-induced cell tumours in the brain...
March 27, 2017: Oncogene
https://www.readbyqxmd.com/read/28346365/an-amylase-like-protein-amyd-is-the-major-negative-regulator-for-%C3%AE-glucan-synthesis-in-aspergillus-nidulans-during-the-asexual-life-cycle
#3
Xiaoxiao He, Shengnan Li, Susan Kaminskyj
α-Glucan affects fungal cell-cell interactions and is important for the virulence of pathogenic fungi. Interfering with production of α-glucan could help to prevent fungal infection. In our previous study, we reported that an amylase-like protein, AmyD, could repress α-glucan accumulation in Aspergillus nidulans. However, the underlying molecular mechanism was not clear. Here, we examined the localization of AmyD and found it was a membrane-associated protein. We studied AmyD function in α-glucan degradation, as well as with other predicted amylase-like proteins and three annotated α-glucanases...
March 27, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28346335/apparent-interfacial-tension-effects-in-protein-stabilized-emulsions-prepared-with-microstructured-systems
#4
Carme Güell, Montserrat Ferrando, Alexandre Trentin, Karin Schroën
Proteins are mostly used to stabilize food emulsions; however, production of protein containing emulsions is notoriously difficult to capture in scaling relations due to the complex behavior of proteins in interfaces, in combination with the dynamic nature of the emulsification process. Here, we investigate premix membrane emulsification and use the Ohnesorge number to derive a scaling relation for emulsions prepared with whey protein, bovine serum albumin (BSA), and a standard emulsifier Tween 20, at various concentrations (0...
March 25, 2017: Membranes
https://www.readbyqxmd.com/read/28346135/polo-like-kinase-dependent-phosphorylation-of-the-synaptonemal-complex-protein-syp-4-regulates-double-strand-break-formation-through-a-negative-feedback-loop
#5
Saravanapriah Nadarajan, Talley J Lambert, Elisabeth Altendorfer, Jinmin Gao, Michael D Blower, Jennifer C Waters, Monica P Colaiácovo
The synaptonemal complex (SC) is an ultrastructurally conserved proteinaceous structure that holds homologous chromosomes together and is required for the stabilization of pairing interactions and the completion of crossover (CO) formation between homologs during meiosis I. Here, we identify a novel role for a central region component of the SC, SYP-4, in negatively regulating formation of recombination-initiating double-strand breaks (DSBs) via a feedback loop triggered by crossover designation in C. elegans...
March 27, 2017: ELife
https://www.readbyqxmd.com/read/28345935/targeting-self-binding-peptides-as-a-novel-strategy-to-regulate-protein-activity-and-function-a-case-study-on-the-proto-oncogene-tyrosine-protein-kinase-c-src
#6
Zhengya Bai, Shasha Hou, Shilei Zhang, Zhongyan Li, Peng Zhou
Previously, we have reported a new biomolecular phenomenon spanning between protein folding and binding, termed as self-binding peptides (SBPs), where a short peptide segment in monomeric protein functions as molecular switch by dynamically binding to/unbinding from its cognate domain in the monomer (Yang C, Zhang S, He P, Wang C, Huang J, Zhou P. Self-binding peptides: folding or binding? J. Chem. Inf. MODEL: 2015, 55: 329-342). Here, we attempt to raise the SBP as a new class of druggable targets to regulate the biological activity and function of proteins...
March 27, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28345916/molecular-mechanism-of-nucleotide-dependent-allosteric-regulation-in-amp-activated-protein-kinase
#7
Navjeet Ahalawat, Rajesh Kumar Murarka
The AMP-activated protein kinase (AMPK), a central enzyme in the regulation of energy homeostasis, is an important drug target for type 2 diabetes, obesity and cancer. Binding of adenosine nucleotides to the regulatory γ-subunit tightly regulates the activity of this enzyme. Though recent crystal structures of AMPK have provided important insights into the allosteric activation of AMPK, molecular details of the regulatory mechanism of AMPK activation is still elusive. Here, we have performed extensive all-atom molecular dynamics (MD) simulations and shown that the kinase domain (KD) and γ-subunit comes closer resulting in a more compact heterotrimeric AMPK complex in AMP-bound state compared to the ATP-bound state...
March 27, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28345907/simulating-protein-mediated-hydrolysis-of-atp-and-other-nucleoside-triphosphates-by-combining-qm-mm-molecular-dynamics-with-advances-in-metadynamics
#8
Rui Sun, Olaseni Sode, James F Dama, Gregory A Voth
The protein mediated hydrolysis of nucleoside triphosphates such as ATP or GTP is one of the most important and challenging biochemical reactions in nature. The chemical environment (water structure, catalytic metal, and amino acid residues) adjacent to the hydrolysis site contains hundreds of atoms, usually greatly limiting the amount of the free energy sampling that one can achieve from computationally demanding electronic structure calculations such as QM/MM simulations. Therefore, the combination of QM/MM molecular dynamics with the recently developed Transition-tempered Metadynamics (TTMetaD), an enhanced sampling method that can provide a high-quality free energy estimate at an early stage in a simulation, is an ideal approach to address the biomolecular nucleoside triphosphate hydrolysis problem...
March 27, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28345889/ape1-accelerates-turnover-of-hogg1-by-preventing-retrograde-binding-to-the-abasic-site-product
#9
Alexandre Esadze, Gaddiel Rodriguez, Shannen Lee Cravens, James T Stivers
A major product of oxidative DNA damage is 8-oxoguanine. In humans, 8-oxoguanine DNA Glycosylase (hOGG1) facilitates removal of these lesions, producing an abasic (AP) site in the DNA that is subsequently incised by AP-endonuclease 1 (APE1). APE1 stimulates turnover of several glycosylases by accelerating rate-limiting product release. However, there have been conflicting accounts of whether hOGG1 follows a similar mechanism. In pre-steady state kinetic measurements, we found that addition of APE1 had no effect on the rapid burst phase of 8-oxoguanine excision by hOGG1, but accelerated steady-state turnover (kcat) by ~10-fold...
March 27, 2017: Biochemistry
https://www.readbyqxmd.com/read/28345879/vibrational-probes-from-small-molecule-solvatochromism-theory-and-experiments-to-applications-in-complex-systems
#10
Bartosz Błasiak, Casey H Londergan, Lauren J Webb, Minhaeng Cho
The vibrational frequency of a chosen normal mode is one of the most accurately measurable spectroscopic properties of molecules in condensed phases. Accordingly, infrared absorption and Raman scattering spectroscopy have provided valuable information on both distributions and ensemble-average values of molecular vibrational frequencies, and these frequencies are now routinely used to investigate structure, conformation, and even absolute configuration of chemical and biological molecules of interest. Recent advancements in coherent time-domain nonlinear vibrational spectroscopy have allowed the study of heterogeneous distributions of local structures and thermally driven ultrafast fluctuations of vibrational frequencies...
March 27, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28345876/engineering-cellular-microenvironments-with-photo-and-enzymatically-responsive-hydrogels-toward-biomimetic-3d-cell-culture-models
#11
Roger Y Tam, Laura J Smith, Molly S Shoichet
Conventional cell culture techniques using 2D polystyrene or glass have provided great insight into key biochemical mechanisms responsible for cellular events such as cell proliferation, differentiation, and cell-cell interactions. However, the physical and chemical properties of 2D culture in vitro are dramatically different than those found in the native cellular microenvironment in vivo. Cells grown on 2D substrates differ significantly from those grown in vivo, and this explains, in part, why many promising drug candidates discovered through in vitro drug screening assays fail when they are translated to in vivo animal or human models...
March 27, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28345864/triple-stage-mass-spectrometry-unravels-the-heterogeneity-of-an-endogenous-protein-complex
#12
Gili Ben-Nissan, Mikhail E Belov, David Morgenstern, Yishai Levin, Orly Dym, Galina Arkind, Carni Lipson, Alexander A Makarov, Michal Sharon
The way we perceive protein complexes is changing. What were once thought to be uniform entities may actually represent an ensemble of different assemblies with distinct functions and regulation. This increased complexity is enabled by the variety of protein diversification mechanisms that exist at every step of the protein biosynthesis pathway, such as alternative splicing and post transcriptional and translational modifications. The resulting variation in subunits can generate compositionally distinct protein assemblies...
March 27, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28345796/establishing-nucleosome-architecture-and-stability-at-promoters-roles-of-pioneer-transcription-factors-and-the-rsc-chromatin-remodeler
#13
REVIEW
Slawomir Kubik, Maria Jessica Bruzzone, David Shore
Improvements in deep sequencing, together with methods to rapidly deplete essential transcription factors (TFs) and chromatin remodelers, have recently led to a more detailed picture of promoter nucleosome architecture in yeast and its relationship to transcriptional regulation. These studies revealed that ∼40% of all budding yeast protein-coding genes possess a unique promoter structure, where we propose that an unusually unstable nucleosome forms immediately upstream of the transcription start site (TSS)...
March 27, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28345718/probing-the-binding-affinity-of-plasma-proteins-adsorbed-on-au-nanoparticles
#14
Xiaoning Zhang, Junting Zhang, Fan Zhang, Shaoning Yu
Nanoparticle (NP) surfaces are modified immediately by the adsorption of proteins when exposed to human blood, leading to the formation of a protein corona. The adsorption of serum proteins is the key process for exploring the bioapplication and biosafety of NPs. In this study, NP-protein binding affinity (Ka) was investigated. Some serum proteins, such as human serum albumin (HSA), trypsin (TRP), hemoglobin (Hb), myoglobin (MB), immunoglobulin G (IgG), carbonic anhydrase (CA), fibrinogen (FIB), chymotrypsin and r-globulin, were used with gold nanoparticles (AuNPs) to address binding affinity according to isothermal titration calorimetry (ITC) combined with dynamic light scattering (DLS) and fluorescence quenching...
March 27, 2017: Nanoscale
https://www.readbyqxmd.com/read/28345664/hierarchical-viscosity-of-aqueous-solution-of-tilapia-scale-collagen-investigated-via-dielectric-spectroscopy-between-500%C3%A2-mhz-and-2-5%C3%A2-thz
#15
H Kawamata, S Kuwaki, T Mishina, T Ikoma, J Tanaka, R Nozaki
Aqueous solutions of biomolecules such as proteins are very important model systems for understanding the functions of biomolecules in actual life processes because interactions between biomolecules and the surrounding water molecules are considered to be important determinants of biomolecules' functions. Globule proteins have been extensively studied via dielectric spectroscopy; the results indicate three relaxation processes originating from fluctuations in the protein molecule, the bound water and the bulk water...
March 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28345052/cardiac-myosin-binding-protein-c-ser-302-phosphorylation-regulates-cardiac-%C3%AE-adrenergic-reserve
#16
Ranganath Mamidi, Kenneth S Gresham, Jiayang Li, Julian E Stelzer
Phosphorylation of cardiac myosin binding protein-C (MyBP-C) modulates cardiac contractile function; however, the specific roles of individual serines (Ser) within the M-domain that are targets for β-adrenergic signaling are not known. Recently, we demonstrated that significant accelerations in in vivo pressure development following β-agonist infusion can occur in transgenic (TG) mouse hearts expressing phospho-ablated Ser(282) (that is, TG(S282A)) but not in hearts expressing phospho-ablation of all three serines [that is, Ser(273), Ser(282), and Ser(302) (TG(3SA))], suggesting an important modulatory role for other Ser residues...
March 2017: Science Advances
https://www.readbyqxmd.com/read/28344973/coarse-grained-conformational-sampling-of-protein-structure-improves-the-fit-to-experimental-hydrogen-exchange-data
#17
Didier Devaurs, Dinler A Antunes, Malvina Papanastasiou, Mark Moll, Daniel Ricklin, John D Lambris, Lydia E Kavraki
Monitoring hydrogen/deuterium exchange (HDX) undergone by a protein in solution produces experimental data that translates into valuable information about the protein's structure. Data produced by HDX experiments is often interpreted using a crystal structure of the protein, when available. However, it has been shown that the correspondence between experimental HDX data and crystal structures is often not satisfactory. This creates difficulties when trying to perform a structural analysis of the HDX data. In this paper, we evaluate several strategies to obtain a conformation providing a good fit to the experimental HDX data, which is a premise of an accurate structural analysis...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28344832/in-silico-functional-elucidation-of-uncharacterized-proteins-of-chlamydia-abortus-strain-llg
#18
Gagandeep Singh, Dixit Sharma, Vikram Singh, Jyoti Rani, Francessco Marotta, Manoj Kumar, Gorakh Mal, Birbal Singh
AIM: This study reports structural modeling, molecular dynamics profiling of hypothetical proteins in Chlamydia abortus genome database. METHODOLOGY: The hypothetical protein sequences were extracted from C. abortus LLG Genome Database for functional elucidation using in silico methods. RESULTS: Fifty-one proteins with their roles in defense, binding and transporting other biomolecules were unraveled. Forty-five proteins were found to be nonhomologous to proteins present in hosts infected by C...
March 2017: Future Science OA
https://www.readbyqxmd.com/read/28344779/accuracy-of-the-detection-of-binding-events-using-3d-single-particle-tracking
#19
Sara Carozza, Jamie Culkin, John van Noort
BACKGROUND: Nanoparticles can be used as markers to track the position of biomolecules, such as single proteins, inside living cells. The activity of a protein can sometimes be inferred from changes in the mobility of the attached particle. Mean Square Displacement analysis is the most common method to obtain mobility information from trajectories of tracked particles, such as the diffusion coefficient D. However, the precision of D sets a limit to discriminate changes in mobility caused by biological events from changes that reflect the stochasticity inherent to diffusion...
2017: BMC Biophysics
https://www.readbyqxmd.com/read/28344778/methodological-advances-in-imaging-intravital-axonal-transport
#20
REVIEW
James N Sleigh, Alessio Vagnoni, Alison E Twelvetrees, Giampietro Schiavo
Axonal transport is the active process whereby neurons transport cargoes such as organelles and proteins anterogradely from the cell body to the axon terminal and retrogradely in the opposite direction. Bi-directional transport in axons is absolutely essential for the functioning and survival of neurons and appears to be negatively impacted by both aging and diseases of the nervous system, such as Alzheimer's disease and amyotrophic lateral sclerosis. The movement of individual cargoes along axons has been studied in vitro in live neurons and tissue explants for a number of years; however, it is currently unclear as to whether these systems faithfully and consistently replicate the in vivo situation...
2017: F1000Research
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