keyword
MENU ▼
Read by QxMD icon Read
search

biomolecular

keyword
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/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
#2
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/28345933/structure-energy-relationships-of-halogen-bonds-in-proteins
#3
Matthew R Scholfield, Melissa Coates Ford, Anna-Carin Cecilia Carlsson, Hawera Butta, Ryan A Mehl, Pui Shing Ho
The structures and stabilities of proteins are defined by a series of weak non-covalent electrostatic, van der Waals, and hydrogen bond (HB) interactions. In this study, we have designed and engineered halogen bonds (XBs) site-specifically in order to study their structure-energy relationship in a model protein, T4 lysozyme. The evidence for XBs is the displacement of the aromatic side chain towards an oxygen acceptor, at distances that are at or less than the sums of their respective van der Waals radii, when the hydroxyl substituent of the wildtype tyrosine is replaced by an iodine...
March 27, 2017: Biochemistry
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
#4
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/28345665/oscillating-electric-field-measures-the-rotation-rate-in-a-native-rotary-enzyme
#5
Csilla-Maria Ferencz, Pál Petrovszki, András Dér, Krisztina Sebők-Nagy, Zoltán Kóta, Tibor Páli
Rotary enzymes are complex, highly challenging biomolecular machines whose biochemical working mechanism involves intersubunit rotation. The true intrinsic rate of rotation of any rotary enzyme is not known in a native, unmodified state. Here we use the effect of an oscillating electric (AC) field on the biochemical activity of a rotary enzyme, the vacuolar proton-ATPase (V-ATPase), to directly measure its mean rate of rotation in its native membrane environment, without any genetic, chemical or mechanical modification of the enzyme, for the first time...
March 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28345343/electronic-and-steric-optimization-of-fluorogenic-probes-for-biomolecular-imaging
#6
Wen Chyan, Henry R Kilgore, Brian Gold, Ronald T Raines
Fluorogenic probes are invaluable tools for spatiotemporal investigations within live cells. In common fluorogenic probes, the intrinsic fluorescence of a small-molecule fluorophore is masked by esterification until entry into a cell, where endogenous esterases catalyze the hydrolysis of the masking groups, generating fluorescence. The susceptibility of masking groups to spontaneous hydrolysis is a major limitation of these probes. Previous attempts to address this problem have incorporated auto-immolative linkers at the cost of atom economy and synthetic adversity...
March 27, 2017: Journal of Organic Chemistry
https://www.readbyqxmd.com/read/28344357/quantum-dot-surface-engineering-toward-inert-fluorophores-with-compact-size-and-bright-stable-emission
#7
Sung Jun Lim, Liang Ma, André Schleife, Andrew M Smith
The surfaces of colloidal nanocrystals are complex interfaces between solid crystals, coordinating ligands, and liquid solutions. For fluorescent quantum dots, the properties of the surface vastly influence the efficiency of light emission, stability, and physical interactions, and thus determine their sensitivity and specificity when they are used to detect and image biological molecules. But after more than 30 years of study, the surfaces of quantum dots remain poorly understood and continue to be an important subject of both experimental and theoretical research...
August 1, 2016: Coordination Chemistry Reviews
https://www.readbyqxmd.com/read/28342983/lipid-quantification-by-raman-microspectroscopy-as-a-potential-biomarker-in-prostate-cancer
#8
Jordan O'Malley, Rahul Kumar, Andrey Kuzmin, Artem Pliss, Neelu Yadav, Srimmitha Balachandar, Jianmin Wang, Kristopher Attwood, Paras N Prasad, Dhyan Chandra
Metastatic castration recurrent prostate cancer (mCRPC) remains incurable and is one of the leading causes of cancer-related death among American men. Therefore, detection of prostate cancer (PCa) at early stages may reduce PCa-related mortality in men. We show that lipid quantification by vibrational Raman Microspectroscopy and Biomolecular Component Analysis may serve as a potential biomarker in PCa. Transcript levels of lipogenic genes including sterol regulatory element-binding protein-1 (SREBP-1) and its downstream effector fatty acid synthase (FASN), and rate-limiting enzyme acetyl CoA carboxylase (ACACA) were upregulated corresponding to both Gleason score and pathologic T stage in the PRAD TCGA cohort...
March 23, 2017: Cancer Letters
https://www.readbyqxmd.com/read/28342228/co-evolutionary-constraints-in-the-sequence-space-of-macromolecular-complexes-reflect-their-self-assembly-pathways
#9
Saurav Mallik, Sudip Kundu
Is the order in which biomolecular subunits self-assemble into functional macromolecular complexes imprinted in their sequence-space? Here we demonstrate that the temporal order of macromolecular complex self-assembly can be efficiently captured using the landscape of residue-level co-evolutionary constraints. This predictive power of co-evolutionary constraints is irrespective of the structural, functional and phylogenetic classification of the complex and of the stoichiometry and quaternary arrangement of the constituent monomers...
March 25, 2017: Proteins
https://www.readbyqxmd.com/read/28341433/minimizing-the-impact-of-joule-heating-as-a-prerequisite-for-the-reliable-analysis-of-metal-protein-complexes-by-capillary-electrophoresis
#10
Paweł Mateusz Nowak, Klaudyna Śpiewak, Michał Woźniakiewicz, Paweł Kościelniak
Herein we report on a drastic release of metal ions from the Fe-bound transferrin, and Fe- or Mn-bound lactoferrin, observed upon the increase in the separation voltage during CE-based analysis. To verify whether this process is caused directly by electric field, we developed an Isothermal Voltage Increase approach (IVI), which is the extension of methods reported by Krylov et al. IVI ensures isothermal conditions while increasing separation voltage by a hydrodynamic pushing of the injected sample to the actively cooled capillary section, combined with a rationale choice of cooling temperature, dependent on the value of current...
March 18, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/28340485/an-approach-for-liposome-immobilization-using-sterically-stabilized-micelles-ssms-as-a-precursor-for-bio-layer-interferometry-based-interaction-studies
#11
Jakob Wallner, Gabriele Lhota, Markus Schosserer, Karola Vorauer-Uhl
Non-fluidic bio-layer interferometry (BLI) has rapidly become a standard tool for monitoring almost all biomolecular interactions in a label-free, real-time and high-throughput manner. High-efficiency screening methods which measure the kinetics of liposomes with a variety of compounds require the immobilization of liposomes. In this work, a method is described for immobilizing liposomes for interaction studies, based on the biophysical principles of this biosensor platform. The immobilization approach includes the loading of DSPE-PEG(2000)-biotin containing sterically stabilized micelles (SSMs) which are restructured in a buffer change step, resulting in an accessible substrate for liposome immobilization...
March 12, 2017: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/28337070/genomic-methods-and-microbiological-technologies-for-profiling-novel-and-extreme-environments-for-the-extreme-microbiome-project-xmp
#12
Scott Tighe, Ebrahim Afshinnekoo, Tara M Rock, Ken McGrath, Noah Alexander, Alexa McIntyre, Sofia Ahsanuddin, Daniela Bezdan, Stefan J Green, Samantha Joye, Sarah Stewart Johnson, Don A Baldwin, Nathan Bivens, Nadim Ajami, Joseph R Carmical, Ian Charold Herriott, Rita Colwell, Mohamed Donia, Jonathan Foox, Nick Greenfield, Tim Hunter, Jessica Hoffman, Joshua Hyman, Ellen Jorgensen, Diana Krawczyk, Jodie Lee, Shawn Levy, Natàlia Garcia-Reyero, Matthew Settles, Kelley Thomas, Felipe Gómez, Lynn Schriml, Nikos Kyrpides, Elena Zaikova, Jon Penterman, Christopher E Mason
The Extreme Microbiome Project (XMP) is a project launched by the Association of Biomolecular Resource Facilities Metagenomics Research Group (ABRF MGRG) that focuses on whole genome shotgun sequencing of extreme and unique environments using a wide variety of biomolecular techniques. The goals are multifaceted, including development and refinement of new techniques for the following: 1) the detection and characterization of novel microbes, 2) the evaluation of nucleic acid techniques for extremophilic samples, and 3) the identification and implementation of the appropriate bioinformatics pipelines...
March 10, 2017: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/28332695/outstanding-reviewers-for-organic-biomolecular-chemistry-in-2016
#13
EDITORIAL
(no author information available yet)
No abstract text is available yet for this article.
March 22, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28330367/multiscale-simulations-of-anisotropic-particles-combining-molecular-dynamics-and-green-s-function-reaction-dynamics
#14
Adithya Vijaykumar, Thomas E Ouldridge, Pieter Rein Ten Wolde, Peter G Bolhuis
The modeling of complex reaction-diffusion processes in, for instance, cellular biochemical networks or self-assembling soft matter can be tremendously sped up by employing a multiscale algorithm which combines the mesoscopic Green's Function Reaction Dynamics (GFRD) method with explicit stochastic Brownian, Langevin, or deterministic molecular dynamics to treat reactants at the microscopic scale [A. Vijaykumar, P. G. Bolhuis, and P. R. ten Wolde, J. Chem. Phys. 143, 214102 (2015)]. Here we extend this multiscale MD-GFRD approach to include the orientational dynamics that is crucial to describe the anisotropic interactions often prevalent in biomolecular systems...
March 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28328543/challenges-in-describing-ribosome-dynamics
#15
Kien Nguyen, Paul Charles Whitford
For decades, protein folding and functional dynamics have been described in terms of diffusive motion across an underlying energy landscape. With continued advances in structural biology and high-performance computing, the field is positioned to extend these approaches to large biomolecular assemblies. Through the application of energy landscape techniques to the ribosome, one may work towards establishing a comprehensive description of the dynamics, which will bridge theoretical concepts and experimental observations...
March 22, 2017: Physical Biology
https://www.readbyqxmd.com/read/28327660/quantitative-volumetric-raman-imaging-of-three-dimensional-cell-cultures
#16
Charalambos Kallepitis, Mads S Bergholt, Manuel M Mazo, Vincent Leonardo, Stacey C Skaalure, Stephanie A Maynard, Molly M Stevens
The ability to simultaneously image multiple biomolecules in biologically relevant three-dimensional (3D) cell culture environments would contribute greatly to the understanding of complex cellular mechanisms and cell-material interactions. Here, we present a computational framework for label-free quantitative volumetric Raman imaging (qVRI). We apply qVRI to a selection of biological systems: human pluripotent stem cells with their cardiac derivatives, monocytes and monocyte-derived macrophages in conventional cell culture systems and mesenchymal stem cells inside biomimetic hydrogels that supplied a 3D cell culture environment...
March 22, 2017: Nature Communications
https://www.readbyqxmd.com/read/28326772/illuminating-the-reaction-pathways-of-viromimetic-assembly
#17
Hande E Cingil, Emre B Boz, Giovanni Biondaro, Renko de Vries, Martien A Cohen Stuart, Daniela J Kraft, Paul van der Schoot, Joris Sprakel
The co-assembly of well-defined biological nanostructures relies on a delicate balance between attractive and repulsive interactions between biomolecular building blocks. Viral capsids are a prototypical example, where coat proteins exhibit not only self-interactions but also interact with the cargo they encapsulate. In Nature the balance between antagonistic and synergistic interactions is evolved to avoid kinetic trapping and polymorphism. To date it has remained a major challenge to experimentally disentangle the complex kinetic reaction pathways that underlie successful co-assembly of biomolecular building blocks in a non-invasive approach with high temporal resolution...
March 22, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28325220/action-of-antibiotic-oxacillin-on-in%C3%A2-vitro-growth-of-methicillin-resistant-staphylococcus-aureus-mrsa-previously-treated-with-homeopathic-medicines
#18
Tânia Aguiar Passeti, Leandro Ribeiro Bissoli, Ana Paula Macedo, Registila Beltrame Libame, Susana Diniz, Silvia Waisse
BACKGROUND: Resistance to antibiotics is a major public health concern worldwide. New treatment options are needed and homeopathy is one such option. We sought to assess the effect of the homeopathic medicine Belladonna (Bell) and a nosode (biotherapy) prepared from a multi-drug resistant bacterial species, methicillin-resistant Staphylococcus aureus (MRSA), on the same bacterium. METHODS: Bell and MRSA nosode were prepared in 6cH and 30cH potencies in 30% alcohol and sterile water, according to the Brazilian Homeopathic Pharmacopeia and tested on MRSA National Collection of Type Cultures (NCTC) 10442...
February 2017: Homeopathy: the Journal of the Faculty of Homeopathy
https://www.readbyqxmd.com/read/28321191/palmitoylethanolamide-reduces-neuropsychiatric-behaviors-by-restoring-cortical-electrophysiological-activity-in-a-mouse-model-of-mild-traumatic-brain-injury
#19
Francesca Guida, Serena Boccella, Monica Iannotta, Danilo De Gregorio, Catia Giordano, Carmela Belardo, Rosaria Romano, Enza Palazzo, Maria A Scafuro, Nicola Serra, Vito de Novellis, Francesco Rossi, Sabatino Maione, Livio Luongo
Traumatic brain injury (TBI) represents a major public health problem, which is associated with neurological dysfunction. In severe or moderate cases of TBI, in addition to its high mortality rate, subjects may encounter diverse behavioral dysfunctions. Previous reports suggest that an association between TBI and chronic pain syndromes tends to be more common in patients with mild forms of brain injury. Despite causing minimal brain damage, mild TBI (mTBI) often leads to persistent psychologically debilitating symptoms, which can include anxiety, various forms of memory and learning deficits, and depression...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/28320943/prion-protein-dynamics-before-aggregation
#20
Kinshuk Raj Srivastava, Lisa J Lapidus
Prion diseases, like Alzheimer's disease and Parkinson disease, are rapidly progressive neurodegenerative disorders caused by misfolding followed by aggregation and accumulation of protein deposits in neuronal cells. Here we measure intramolecular polypeptide backbone reconfiguration as a way to understand the molecular basis of prion aggregation. Our hypothesis is that when reconfiguration is either much faster or much slower than bimolecular diffusion, biomolecular association is not stable, but as the reconfiguration rate becomes similar to the rate of biomolecular diffusion, the association is more stable and subsequent aggregation is faster...
March 20, 2017: Proceedings of the National Academy of Sciences of the United States of America
keyword
keyword
54480
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"