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https://www.readbyqxmd.com/read/28938109/investigating-mutation-specific-biological-activities-of-small-molecules-using-quantitative-structure-activity-relationship-for-epidermal-growth-factor-receptor-in-cancer
#1
P Anoosha, R Sakthivel, M Michael Gromiha
Epidermal Growth Factor Receptor (EGFR) is a potential drug target in cancer therapy. Missense mutations play major roles in influencing the protein function, leading to abnormal cell proliferation and tumorigenesis. A number of EGFR inhibitor molecules targeting ATP binding domain were developed for the past two decades. Unfortunately, they become inactive due to resistance caused by new mutations in patients, and previous studies have also reported noticeable differences in inhibitor binding to distinct known driver mutants as well...
August 26, 2017: Mutation Research
https://www.readbyqxmd.com/read/28937982/protein-complex-prediction-via-dense-subgraphs-and-false-positive-analysis
#2
Cecilia Hernandez, Carlos Mella, Gonzalo Navarro, Alvaro Olivera-Nappa, Jaime Araya
Many proteins work together with others in groups called complexes in order to achieve a specific function. Discovering protein complexes is important for understanding biological processes and predict protein functions in living organisms. Large-scale and throughput techniques have made possible to compile protein-protein interaction networks (PPI networks), which have been used in several computational approaches for detecting protein complexes. Those predictions might guide future biologic experimental research...
2017: PloS One
https://www.readbyqxmd.com/read/28937829/nonlinearity-coherence-and-complexity-biophysical-aspects-related-to-health-and-disease
#3
Alberto Foletti, Larissa Brizhik
Biological organisms are complex open dissipative systems whose dynamical stability is sustained due to the exchange of matter, energy and information. Dynamical stability occurs through a number of mechanisms that sustain efficient adaptive dynamics. Such properties of living matter can be the consequence of a self-consistent state of matter and electromagnetic field (EMF). Based on the soliton model of charge transport in redox processes, we describe a possible mechanism of the origin of endogenous EMF and coherence...
September 22, 2017: Electromagnetic Biology and Medicine
https://www.readbyqxmd.com/read/28937740/ab-initio-study-of-the-atomic-level-structure-of-the-rutile-tio2-110-titanium-nitride-tin-interface
#4
Jose Julio Gutierrez Moreno, Michael Nolan
Titanium nitride (TiN) is widely used in industry as a protective coating due to its hardness and resistance to corrosion and can spontaneously form a thin oxide layer when it is exposed to air, which could modify the properties of the coating. With limited understanding of the TiO2 - TiN interfacial system at present, this work aims to describe the structural and electronic properties of oxidized TiN based on a density functional theory (DFT) study of the rutile TiO2 (110) - TiN (100) interface model system, also including Hubbard +U correction on Ti 3d states...
September 22, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28937227/low-temperature-decoupling-of-water-and-protein-dynamics-measured-by-neutron-scattering
#5
Antonio Benedetto
Water plays a major role in bio-systems, greatly contributing to determine their structure, stability and function. It is well know, for instance, that proteins require a minimum amount of water to be fully functional. Despite many years of intensive research, however, the detailed nature of protein-hydration water interactions is still partly unknown. The widely-accepted "protein dynamical transition" scenario is based on perfect coupling between the dynamics of proteins and that of their hydration water, which has never been probed in depth experimentally...
September 22, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28936512/magnetic-janus-particles-synthesized-using-droplet-micro-magnetofluidic-techniques-for-protein-detection
#6
V B Varma, R G Wu, Z P Wang, R V Ramanujan
Magnetic droplets on a microfluidic platform can act as micro-robots, providing wireless, remote, and programmable control. This field of droplet micro-magnetofluidics (DMMF) is useful for droplet merging, mixing and synthesis of Janus structures. Specifically, magnetic Janus particles (MJP) are useful for protein and DNA detection as well as magnetically controlled bioprinting. However, synthesis of MJP with control of the functional phases is a challenge. Hence, we developed a high flow rate, surfactant-free, wash-less method to synthesize MJP by integration of DMMF with hybrid magnetic fields...
September 22, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/28936206/an-in-vitro-fermentation-study-on-the-effects-of-gluten-friendly-tm-bread-on-microbiota-and-short-chain-fatty-acids-of-fecal-samples-from-healthy-and-celiac-subjects
#7
Adele Costabile, Triana Bergillos-Meca, Loretta Landriscina, Antonio Bevilacqua, Isidro Gonzalez-Salvador, Maria R Corbo, Leonardo Petruzzi, Milena Sinigaglia, Carmela Lamacchia
Recently, an innovative gluten detoxification method called Gluten Friendly(TM) (GF) has been developed. It induces structural modifications, which abolish the antigenic capacity of gluten and reduce the in vitro immunogenicity of the most common epitopes involved in celiac disease, without compromising the nutritional and technological properties. This study investigated the in vitro effects of GF bread (GFB) on the fecal microbiota from healthy and celiac individuals by a three-stage continuous fermentative system, which simulates the colon (vessel 1, proximal colon; vessel 2, transverse colon; and vessel 3, distal colon), as well as on the production of short chain fatty acids (SCFA, acetate, propionate, butyrate)...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28936204/modulatory-influence-of-segmented-filamentous-bacteria-on-transcriptomic-response-of-gnotobiotic-mice-exposed-to-tcdd
#8
Robert D Stedtfeld, Benli Chai, Robert B Crawford, Tiffany M Stedtfeld, Maggie R Williams, Shao Xiangwen, Tomomi Kuwahara, James R Cole, Norbert E Kaminski, James M Tiedje, Syed A Hashsham
Environmental toxicants such as 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), an aryl hydrocarbon receptor (AhR), are known to induce host toxicity and structural shifts in the gut microbiota. Key bacterial populations with similar or opposing functional responses to AhR ligand exposure may potentially help regulate expression of genes associated with immune dysfunction. To examine this question and the mechanisms for AhR ligand-induced bacterial shifts, C57BL/6 gnotobiotic mice were colonized with and without segmented filamentous bacteria (SFB) - an immune activator...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28935764/ubiquitin-recognition-of-bap1-understanding-its-enzymatic-function
#9
Pranita Hanpude, Sushmita Bhattacharya, Abhishek Kumar Singh, Tushar Kanti Maiti
BRCA1 associated protein 1 (BAP1) is a nuclear localizing UCH, having tumor suppressor activity and is widely involved in many crucial cellular processes. BAP1 has garnered attention for its links with cancer, however, the molecular mechanism in the regulation of cancer by BAP1 has not been established. Among the four UCHs, only BAP1 and UCHL5 are able to hydrolyze small and large ubiquitin adducts but UCHL5 hydrolyzes only when it is present in the PA700 complex of the proteasome. The ability of BAP1 to cleave large ubiquitin derivatives is because of its relatively longer active-site crossover loop than other UCHs...
September 21, 2017: Bioscience Reports
https://www.readbyqxmd.com/read/28935684/rack1-function-in-intestinal-epithelia-regulating-crypt-cell-proliferation-and-regeneration-and-promoting-differentiation-and-apoptosis
#10
Zhuan-Fen Cheng, Reetesh K Pai, Christine A Cartwright
Previously we showed that Rack1 (Receptor for Activated C Kinase) regulates growth of colon cells in vitro, partly by suppressing Src kinase activity at key cell cycle checkpoints, in apoptotic and cell survival pathways and at cell-cell adhesions. Here, we generated mouse models of Rack1 deficiency to assess Rack1's function in intestinal epithelia in vivo Intestinal Rack1 deficiency resulted in proliferation of crypt cells, diminished differentiation of crypt cells into enterocyte, goblet and enteroendocrine cell lineages and expansion of Paneth cell populations...
September 21, 2017: American Journal of Physiology. Gastrointestinal and Liver Physiology
https://www.readbyqxmd.com/read/28935566/construction-of-protein-functionalized-virus-like-particles-of-parvovirus-b19
#11
Ismael Bustos-Jaimes, Ricardo Arturo Soto-Román, Isabel Alejandra Gutiérrez-Landa, Josefina Valadez-García, Carla Lizbeth Segovia-Trinidad
Decoration of virus-like particles (VLPs) expands the repertory of functions these particles can display. In the last years, VLPs have successfully been used as scaffolds to present different molecules, frequently through the specific reaction of chemical groups on the surface of the particles, or by protein engineering when the presentation of peptides or proteins is the primary goal. VLPs of parvovirus B19 (B19V), have been previously produced in vitro and its stability and ability to assemble into hybrid particles composed of wild-type and chimeric proteins evidenced their potential as research tools...
September 18, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28935370/the-hierarchical-structure-of-the-perichromosomal-layer-comprises-ki67-ribosomal-rnas-and-nucleolar-proteins
#12
Yuki Hayashi, Kazashi Kato, Keiji Kimura
The perichromosomal layer (PCL) is a structure that surrounds mitotic chromosomes, found in both animal and plant cells. It comprises various proteins and RNAs, mainly derived from the nucleolus. Several functions for the PCL have been suggested; however, the mechanism of PCL organization during mitosis remains unclear. The localization of several nucleolar proteins to the PCL is reportedly dependent on pre-ribosomal RNAs and the marker of proliferation, Ki67, which is a major PCL-localized protein. Here we demonstrate that, although the removal of pre-ribosomal RNAs from the PCL causes PCL delocalization of several nucleolar proteins, it does not affect the localization of Ki67...
September 18, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28935369/a-three-dimensional-model-of-rnase-p-in-the-hyperthermophilic-archaeon-pyrococcus-horikoshii-ot3
#13
Xuzhu Gao, Kosuke Oshima, Toshifumi Ueda, Takashi Nakashima, Makoto Kimura
Ribonuclease P (RNase P) is an endoribonuclease involved in maturation of the 5'-end of tRNA. We found previously that RNase P in the hyperthermophilic archaeon Pyrococcus horikoshii OT3 consists of a catalytic RNase P RNA (PhopRNA) and five protein cofactors designated PhoPop5, PhoRpp21, PhoRpp29, PhoRpp30, and PhoRpp38. The crystal structures of the five proteins have been determined, a three-dimensional (3-D) model of PhopRNA has been constructed, and biochemical data, including protein-RNA interaction sites, have become available...
September 18, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28935265/quinazolinone-based-rhodanine-3-acetic-acids-as-potent-aldose-reductase-inhibitors-synthesis-functional-evaluation-and-molecular-modeling-study
#14
Sherihan El-Sayed, Kamel Metwally, Abdalla A El-Shanawani, Lobna M Abdel-Aziz, Ahmed A El-Rashedy, Mahmoud E S Soliman, Luca Quattrini, Vito Coviello, Concettina la Motta
A series of quinazolinone-based rhodanine-3-acetic acids was synthesized and tested for in vitro aldose reductase inhibitory activity. All the target compounds displayed nanomolar activity against the target enzyme. Compounds 3a, 3b, and 3e exhibited almost 3-fold higher activity as compared to the only marketed reference drug epalrestat. Structure-activity relationship studies indicated that bulky substituents at the 3-phenyl ring of the quinazolinone moiety are generally not tolerated in the active site of the enzyme...
August 24, 2017: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/28935133/functional-validation-of-heteromeric-kainate-receptor-models
#15
Teresa Paramo, Patricia M G E Brown, Maria Musgaard, Derek Bowie, Philip C Biggin
Kainate receptors require the presence of external ions for gating. Most work thus far has been performed on homomeric GluK2 but, in vivo, kainate receptors are likely heterotetramers. Agonists bind to the ligand-binding domain (LBD) which is arranged as a dimer of dimers as exemplified in homomeric structures, but no high-resolution structure currently exists of heteromeric kainate receptors. In a full-length heterotetramer, the LBDs could potentially be arranged either as a GluK2 homomer alongside a GluK5 homomer or as two GluK2/K5 heterodimers...
September 19, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28934966/effectiveness-of-an-interactive-telerehabilitation-system-with-home-based-exercise-training-in-patients-after-total-hip-or-knee-replacement-study-protocol-for-a-multicenter-superiority-no-blinded-randomized-controlled-trial
#16
Sarah Eichler, Sophie Rabe, Annett Salzwedel, Steffen Müller, Josefine Stoll, Nina Tilgner, Michael John, Karl Wegscheider, Frank Mayer, Heinz Völler
BACKGROUND: Total hip or knee replacement is one of the most frequently performed surgical procedures. Physical rehabilitation following total hip or knee replacement is an essential part of the therapy to improve functional outcomes and quality of life. After discharge from inpatient rehabilitation, a subsequent postoperative exercise therapy is needed to maintain functional mobility. Telerehabilitation may be a potential innovative treatment approach. We aim to investigate the superiority of an interactive telerehabilitation intervention for patients after total hip or knee replacement, in comparison to usual care, regarding physical performance, functional mobility, quality of life and pain...
September 21, 2017: Trials
https://www.readbyqxmd.com/read/28934872/a-structural-equation-model-of-patient-healthcare-provider-relationships-and-hiv-infected-patient-outcomes-in-chinese-populations
#17
Wei-Ti Chen, Chengshi Shiu, Joyce P Yang, Peing Chuang, Lin Zhang, Meijuan Bao, Hongzhou Lu
Obtaining maximum antiretroviral therapy (ART) adherence is critical for maintaining a high CD4 count and strong immune function in PLWHA. Key factors for achieving optimum adherence include good medication self-efficacy, decreased medication-taking difficulties, and positive patient-healthcare provider (HCP) relationships. Limited studies have analyzed the correlation of these factors and ART adherence in Chinese population. In this paper, structural equation modeling was performed to assess the proposed model of relations between patient-HCP relationships and adherence...
September 21, 2017: AIDS Care
https://www.readbyqxmd.com/read/28934700/copper-ii-complex-with-6-methylpyridine-2-carboxyclic-acid-experimental-and-computational-study-on-the-xrd-ft-ir-and-uv-vis-spectra-refractive-index-band-gap-and-nlo-parameters
#18
Sümeyye Altürk, Davut Avcı, Adil Başoğlu, Ömer Tamer, Yusuf Atalay, Necmi Dege
Crystal structure of the synthesized copper(II) complex with 6-methylpyridine-2-carboxylic acid, [Cu(6-Mepic)2·H2O]·H2O, was determined by XRD, FT-IR and UV-Vis spectroscopic techniques. Furthermore, the geometry optimization, harmonic vibration frequencies for the Cu(II) complex were carried out by using Density Functional Theory calculations with HSEh1PBE/6-311G(d,p)/LanL2DZ level. Electronic absorption wavelengths were obtained by using TD-DFT/HSEh1PBE/6-311G(d,p)/LanL2DZ level with CPCM model and major contributions were determined via Swizard/Chemissian program...
September 18, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/28934693/enzyme-classification-using-multiclass-support-vector-machine-and-feature-subset-selection
#19
Debasmita Pradhan, Sudarsan Padhy, Biswajit Sahoo
Proteins are the macromolecules responsible for almost all biological processes in a cell. With the availability of large number of protein sequences from different sequencing projects, the challenge with the scientist is to characterize their functions. As the wet lab methods are time consuming and expensive, many computational methods such as FASTA, PSI-BLAST, DNA microarray clustering, and Nearest Neighborhood classification on protein-protein interaction network have been proposed. Support vector machine is one such method that has been used successfully for several problems such as protein fold recognition, protein structure prediction etc...
August 31, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28934492/concerted-action-of-two-3-cap-independent-translation-enhancers-increases-the-competitive-strength-of-translated-viral-genomes
#20
Zhiyou Du, Olga M Alekhina, Konstantin S Vassilenko, Anne E Simon
Several families of plant viruses evolved cap-independent translation enhancers (3'CITE) in the 3' untranslated regions of their genomic (g)RNAs to compete with ongoing cap-dependent translation of cellular mRNAs. Umbravirus Pea enation mosaic virus (PEMV)2 is the only example where three 3'CITEs enhance translation: the eIF4E-binding Panicum mosaic virus-like translational enhancer (PTE) and ribosome-binding 3' T-shaped structure (TSS) have been found in viruses of different genera, while the ribosome-binding kl-TSS that provides a long-distance interaction with the 5' end is unique...
September 19, 2017: Nucleic Acids Research
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