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https://www.readbyqxmd.com/read/27936519/a-computational-approach-for-studying-antibody-antigen-interactions-without-prior-structural-information-the-anti-testosterone-binding-antibody-as-a-case-study
#1
Artturi Koivuniemi, Kristiina Takkinen, Tarja Nevanen
Given the increasing exploitation of antibodies in different contexts such as molecular diagnostics and therapeutics, it would be beneficial to unravel the atomistic level properties of antibody-antigen complexes with the help of computational modeling. Thus, here we have studied the feasibility of computational tools to gather atomic scale information regarding the antibody-antigen complexes solely starting from an amino acid sequence. First, we constructed a homology model for the anti-testosterone binding antibody based on the knowledge based classification of complementary determining regions (CDRs) and implicit solvent molecular dynamics simulations...
December 9, 2016: Proteins
https://www.readbyqxmd.com/read/27936518/computational-investigation-of-proton-transfer-pka-shifts-and-ph-optimum-of-protein-dna-and-protein-rna-complexes
#2
Yunhui Peng, Emil Alexov
Protein-nucleic acid interactions play a crucial role in many biological processes. This work investigates the changes of pKa values and protonation states of ionizable groups (including nucleic acid bases) that may occur at protein-nucleic acid binding. Taking advantage of the recently developed pKa calculation tool DelphiPka, we utilize the large protein-nucleic acid interaction database (NPIDB database) to model pKa shifts caused by binding. It has been found that the protein's interfacial basic residues experience favorable electrostatic interactions while the protein acidic residues undergo proton uptake to reduce the energy cost upon the binding...
December 9, 2016: Proteins
https://www.readbyqxmd.com/read/27936513/probing-the-structural-dynamics-of-the-crispr-cas9-rna-guided-dna-cleavage-system-by-coarse-grained-modeling
#3
Wenjun Zheng
In the adaptive immune systems of many bacteria and archaea, the Cas9 endonuclease forms a complex with specific guide/scaffold RNA to identify and cleave complementary target sequences in foreign DNA. This DNA targeting machinery has been exploited in numerous applications of genome editing and transcription control. However, the molecular mechanism of the Cas9 system is still obscure. Recently, high-resolution structures have been solved for Cas9 in different structural forms (e.g., unbound forms, RNA-bound binary complexes, and RNA-DNA-bound tertiary complexes, corresponding to an inactive state, a pre-target-bound state, and a cleavage-competent or product state), which offered key structural insights to the Cas9 mechanism...
December 9, 2016: Proteins
https://www.readbyqxmd.com/read/27936490/combining-ancestral-sequence-reconstruction-with-protein-design-to-identify-an-interface-hotspot-in-a-key-metabolic-enzyme-complex
#4
Alexandra Holinski, Kristina Heyn, Rainer Merkl, Reinhard Sterner
It is important to identify hotspot residues that determine protein-protein interactions in interfaces of macromolecular complexes. We have applied a combination of ancestral sequence reconstruction and protein design to identify hotspots within imidazole glycerol phosphate synthase (ImGPS). ImGPS is a key metabolic enzyme complex, which links histidine and de novo purine biosynthesis and consists of the cyclase subunit HisF and the glutaminase subunit HisH. Initial fluorescence titration experiments showed that HisH from Zymomonas mobilis (zmHisH) binds with high affinity to the reconstructed HisF from the last universal common ancestor (LUCA-HisF) but not to HisF from Pyrobaculum arsenaticum (paHisF), which differ by 103 residues...
December 9, 2016: Proteins
https://www.readbyqxmd.com/read/27936436/spectroscopic-single-crystal-x-ray-hirshfeld-in-vitro-and-in-silico-biological-evaluation-of-a-new-series-of-potent-thiazole-nucleus-integrated-with-pyrazoline-scaffolds
#5
Vinutha V Salian, Badiadka Narayana, Balladka K Sarojini, Madan S Kumar, Govinahalli S Nagananda, Kullaiah Byrappa, Avinash K Kudva
In the present study, the spectroscopic characterization of a new series of substituted thiazole linked pyrazoline scaffolds 4a-l was performed. The formation of 4a-l from the intermediate 3-(4-chlorophenyl)-5-[4-(propan-2-yl)phenyl]-4,5-dihydro-1H-pyrazole-1-carbothioamide 2 and substituted 2-bromo-1-phenylethanone 3a-l was evidenced through the changes in FTIR, (1)H NMR, (13)C NMR, LCMS data. The X-ray diffraction studies revealed that compound 2 and 4g crystallized in monoclinic crystal system with P21/n space group...
November 28, 2016: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/27936414/-am-i-too-emotional-for-this-job-an-exploration-of-student-midwives-experiences-of-coping-with-traumatic-events-in-the-labour-ward
#6
Liz Coldridge, Sarah Davies
BACKGROUND: midwifery is emotionally challenging work, and learning to be a midwife brings its own particular challenges. For the student midwife, clinical placement in a hospital labour ward is especially demanding. In the context of organisational tensions and pressures the experience of supporting women through the unpredictable intensity of the labour process can be a significant source of stress for student midwives. Although increasing attention is now being paid to midwives' traumatic experiences and wellbeing few researchers have examined the traumatic experiences of student midwives...
November 28, 2016: Midwifery
https://www.readbyqxmd.com/read/27936401/adsorptive-removal-and-separation-of-chemicals-with-metal-organic-frameworks-contribution-of-%C3%AF-complexation
#7
REVIEW
Nazmul Abedin Khan, Sung Hwa Jhung
Efficient removal and separation of chemicals from the environment has become a vital issue from a biological and environmental point of view. Currently, adsorptive removal/separation is one of the most promising approaches for cleaning purposes. Selective adsorption/removal of various sulfur- and nitrogen-containing compounds, olefins, and π-electron-rich gases via π-complex formation between an adsorbent and adsorbate molecules is very competitive. Porous metal-organic framework (MOF) materials are very promising in the adsorption/separation of various liquids and gases owing to their distinct characteristics...
November 27, 2016: Journal of Hazardous Materials
https://www.readbyqxmd.com/read/27936397/design-of-a-new-comprehensive-continuous-monitoring-system-for-environmental-radioactive-aerosol
#8
Hongkun Xu, Zihan Huang, Ge Wang, Changli Mu, Yin Yin
In order to comprehensive monitoring the radioactive isotopes from nuclear facilities, we developed a dual channel spectral monitoring instrument, and realized synchronous measurement for alpha, beta and gamma radionuclides. This article focuses on how to ensure its accuracy, stability and efficiency. First is the accuracy. In order to lower the interference of environmental and detector performance variation, the zero phase shift filter was designed to ensure the accuracy of characteristic peak position. Lorenz fitting algorithm was designed to reduce the effect of spectral low-energy tailing...
December 1, 2016: Applied Radiation and Isotopes
https://www.readbyqxmd.com/read/27936358/moving-beyond-simple-answers-to-complex-questions-how-does-context-affect-alcohol-s-role-in-sexual-assault-perpetration-a-commentary-on-testa-and-cleveland-2017
#9
Antonia Abbey
No abstract text is available yet for this article.
January 2017: Journal of Studies on Alcohol and Drugs
https://www.readbyqxmd.com/read/27936336/experiences-of-health-professionals-caring-for-people-presenting-to-the-emergency-department-after-taking-crystal-methamphetamine-ice
#10
Michelle Cleary, Debra Jackson, Cindy Woods, Rachel Kornhaber, Jan Sayers, Kim Usher
Globally, addiction to "ICE" (crystal methamphetamine) is increasing and presents emergency health care services personnel with a number of challenges. This paper reports the first of two major themes arising from a qualitative study investigating health professionals' experiences' managing people presenting to the Emergency Department (ED) after taking "ICE." The theme "Caring for people who use 'ICE' when presenting to EDs" comprises five subthemes. These are: (a) expecting the unexpected: "they're just off their heads"; (b) complexity of care: "underlying trauma and emotional dysregulation";...
December 9, 2016: Issues in Mental Health Nursing
https://www.readbyqxmd.com/read/27936321/stability-of-a-transient-protein-complex-in-a-charged-aqueous-droplet-with-variable-ph
#11
Myong In Oh, Styliani Consta
Electrospray ionization mass spectrometry (ESI-MS) has the potential to become a high-throughput robust experimental method for the detection of protein-protein equilibrium constants. Poorly understood processes that affect the stability of weak non-covalent protein complexes in the intervening droplet environment is a significant factor that precludes the advancement of the method. We use molecular dynamics to study the stability of a ubiquitin and ubiquitin-associated domain complex (RCSB PDB code 2MRO) in an aqueous droplet with changing size and charge concentration...
December 9, 2016: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/27936313/knight-shift-in-13-c%C3%A2-nmr-resonances-confirms-the-coordination-of-n-heterocyclic-carbene-ligands-to-water-soluble-palladium-nanoparticles
#12
Juan M Asensio, Simon Tricard, Yannick Coppel, Román Andrés, Bruno Chaudret, Ernesto de Jesús
The coordination of N-heterocyclic carbene (NHC) ligands to the surface of 3.7 nm palladium nanoparticles (PdNPs) can be unambiguously established by observation of Knight shift (KS) in the (13) C resonance of the carbenic carbon. In order to validate this coordination, PdNPs with sizes ranging from 1.3 to 4.8 nm were prepared by thermal decomposition or reduction with CO of a dimethyl NHC Pd(II) complex. NMR studies after (13) CO adsorption established that the KS shifts the (13) C resonances of the chemisorbed molecules several hundreds of ppm to high frequencies only when the particle exceeds a critical size of around 2 nm...
December 9, 2016: Angewandte Chemie
https://www.readbyqxmd.com/read/27936312/synthesis-characterization-and-computational-analysis-of-the-dialanate-dianion-h3-al-alh3-2-a-valence-isoelectronic-analogue-of-ethane
#13
Simon J Bonyhady, Nicole Holzmann, Gernot Frenking, Andreas Stasch, Cameron Jones
The first example of a well-defined binary, low-oxidation-state aluminum hydride species that is stable at ambient temperature, namely the dianion in [{((Dep) Nacnac)Mg}2 (μ-H)]2 [H3 Al-AlH3 ] ((Dep) Nacnac=[(DepNCMe)2 CH](-) , Dep=2,6-diethylphenyl), has been prepared via a magnesium(I) reduction of the alanate complex, ((Dep) Nacnac)Mg(μ-H)3 AlH(NEt3 ). An X-ray crystallographic analysis has shown the compound to be a contact ion complex, which computational studies have revealed to be the source of the stability of the aluminum(II) dianion...
December 9, 2016: Angewandte Chemie
https://www.readbyqxmd.com/read/27936304/continuous-flow-synthesis-and-purification-of-aryldiazomethanes-through-hydrazone-fragmentation
#14
Éric Lévesque, Simon T Laporte, André B Charette
Electron-rich diazo compounds, such as aryldiazomethanes, are powerful reagents for the synthesis of complex structures, but the risks associated with their toxicity and instability often limit their use. Flow chemistry techniques make these issues avoidable, as the hazardous intermediate can be used as it is produced, avoiding accumulation and handling. Unfortunately, the produced stream is often contaminated with other reagents and by-products, making it incompatible with many applications, especially in catalysis...
December 9, 2016: Angewandte Chemie
https://www.readbyqxmd.com/read/27936301/new-furanone-derivatives-and-alkaloids-from-the-co-culture-of-marine-derived-fungi-aspergillus-sclerotiorum-and-penicillium-citrinum
#15
Jie Bao, Jie Wang, Xiao-Yong Zhang, Xu-Hua Nong, Shu-Hua Qi
Six new compounds including two furanone derivatives sclerotiorumins A-B (1-2), one novel oxadiazin derivative sclerotiorumin C (3), one pyrrole derivative 1-(4-benzyl-1H-pyrrol-3-yl)ethanone (4), and two complexes of neoaspergillic acid aluminiumneohydroxyaspergillin (5) and ferrineohydroxyaspergillin (6) were isolated from the co-culture of marine-derived fungi Aspergillus sclerotiorum and Penicillium citrinum. Compound 3 was the first natural 1,2,4-oxadiazin-6-one. Compound 5 showed significant and selective cytotoxicity against human histiocytic lymphoma U937 cell line (IC50 = 4...
December 9, 2016: Chemistry & Biodiversity
https://www.readbyqxmd.com/read/27936297/aiegen-with-fluorescence-phosphorescence-dual-mechanoluminescence-at-room-temperature
#16
Jie Yang, Zichun Ren, Zongliang Xie, Yingjie Liu, Can Wang, Yujun Xie, Qian Peng, Bin Xu, Wenjing Tian, Fan Zhang, Zhenguo Chi, Qianqian Li, Zhen Li
We report the first example of an AIEgen (DPP-BO) with fluorescence-phosphorescence dual emission under mechanical stimulation. By carefully analyzing the crystal structure of DPP-BO, the efficient intermolecular and intramolecular interactions should account for its unique mechanoluminescence (ML) properties, especially the abnormal phosphorescence, as further confirmed by controlled experiments and theoretical calculations for the presence of ISC transitions. These results provide important information for understanding the complex ML process, possibly opening up a new way to study the inherent mechanism of ML by broadening the application of AIEgens...
December 9, 2016: Angewandte Chemie
https://www.readbyqxmd.com/read/27936296/antiangiogenic-and-toxic-effects-of-genistein-usnic-acid-and-their-copper-complexes-in-zebrafish-embryos-at-different-developmental-stages
#17
Heidrun Draut, Tobias Rehm, Gerrit Begemann, Rainer Schobert
Angiogenesis plays a major role in the normal embryonic development and in diseases such as cancer. Drugs that control angiogenesis are an alternative way to tackle this disease. The polyphenols usnic acid 3, genistein 5, and daidzein 6 were tested for antiangiogenic and unwanted effects in zebrafish embryos whose blood vessel system resembles that of mammals. The established tyrosine kinase inhibitors axitinib 1 and tyrphostin AG490 2 were included for comparison. All compounds except 6 caused distinct antiangiogenic effects such as a concentration-dependent reduction of intersegmental vessels, dorsal longitudinal anastomotic vessels, subintestinal veins and secondary sprouts...
December 9, 2016: Chemistry & Biodiversity
https://www.readbyqxmd.com/read/27936294/disulfide-catalyzed-visible-light-mediated-oxidative-cleavage-of-c-c-bonds-and-evidence-of-an-olefin-disulfide-charge-transfer-complex
#18
Yuchao Deng, Xiao-Jing Wei, Hui Wang, Yuhan Sun, Timothy Noël, Xiao Wang
A photocatalytic method for the aerobic oxidative cleavage of C=C bonds has been developed. Electron-rich aromatic disulfides were employed as photocatalyst. Upon visible-light irradiation, typical mono- and multi-substituted aromatic olefins could be converted into ketones and aldehydes at ambient temperature. Experimental and computational studies suggest that a disulfide-olefin charge-transfer complex is possibly responsible for the unconventional dissociation of S-S bond under visible light.
December 9, 2016: Angewandte Chemie
https://www.readbyqxmd.com/read/27936289/anisotropic-change-in-the-magnetic-susceptibility-of-a-dynamic-single-crystal-of-a-cobalt-ii-complex
#19
Zi-Shuo Yao, Shu-Qi Wu, Yasutaka Kitagawa, Sheng-Qun Su, You-Gui Huang, Guo-Ling Li, Zhong-Hai Ni, Hiroyuki Nojiri, Yoshihito Shiota, Kazunari Yoshizawa, Soonchul Kang, Shinji Kanegawa, Osamu Sato
Atypically anisotropic and large changes in magnetic susceptibility, along with a change in crystalline shape, were observed in a Co(II) complex at near room temperature. This was achieved by combining oxalate molecules, acting as rotor, and a Co(II) ion with unquenched orbital angular momentum. A thermally controlled 90° rotation of the oxalate counter anion triggered a symmetry-breaking ferroelastic phase transition, accompanied by contraction-expansion behavior (ca. 4.5 %) along the long axis of a rod-like single crystal...
December 9, 2016: Angewandte Chemie
https://www.readbyqxmd.com/read/27936282/metabolomic-data-suggest-regulation-of-black-howler-monkey-alouatta-pigra-diet-composition-at-the-molecular-level
#20
Katherine R Amato, Alexander Ulanov, Kou-San Ju, Paul A Garber
In addition to macronutrients, foods consist of a complex set of chemical compounds that can influence dietary selectivity and consumer physiology. Metabolomics allow us to describe this complexity by quantifying all small molecules, or metabolites, in a food item. In this study we use GC-MS based metabolomics to describe the metabolite profiles of foods consumed by one population of Mexican black howler monkeys (Alouatta pigra) over a 10-month period. Our data indicate that each food exhibited a distinct metabolite profile, and the average weekly intake of metabolites such as neochlorogenic acid and serotonin (5-hydroxytryptamine) was correlated with the consumption of certain plant parts...
December 9, 2016: American Journal of Primatology
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