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https://www.readbyqxmd.com/read/28088125/computational-methods-for-analyzing-conformational-variability-of-macromolecular-complexes-from-cryo-electron-microscopy-images
#1
REVIEW
Slavica Jonić
Thanks to latest technical advances in cryo-electron microscopy (cryo-EM), structures of macromolecular complexes (viruses, ribosomes, etc.) are now often obtained at near-atomic resolution. Also, studies of conformational changes of complexes, in connection with their function, are gaining ground. Conformational variability analysis is usually done by classifying images in a number of discrete classes supposedly representing all conformational states present in the specimen. However, discrete classes cannot be meaningfully defined when the conformational change is continuous (the specimen contains a continuum of states instead of a few discrete states)...
January 11, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28088083/specificity-and-stability-of-transient-protein-protein-interactions
#2
REVIEW
Sneha Vishwanath, Anshul Sukhwal, Ramanathan Sowdhamini, Narayanaswamy Srinivasan
Remarkable features that are achieved in a protein-protein complex to precise levels are stability and specificity. Deviation from the normal levels of specificity and stability, which is often caused by mutations, could result in disease conditions. Chemical nature, 3-D arrangement and dynamics of interface residues code for both specificity and stability. This article reviews roles of interfacial residues in transient protein-protein complexes. It is proposed that aside from hotspot residues conferring stability to the complex, a small set of 'rigid' residues at the interface that maintain conformation between complexed and uncomplexed forms, play a major role in conferring specificity...
January 11, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28088082/nature-of-phase-transitions-in-ammonium-oxofluorovanadates-a-vibrational-spectroscopy-study-of-nh4-3vo2f4-and-nh4-3vof5
#3
REVIEW
Yu V Gerasimova, A S Oreshonkov, N M Laptash, A N Vtyurin, A S Krylov, N P Shestakov, A A Ershov, A G Kocharova
Two ammonium oxofluorovanadates, (NH4)3VO2F4 and (NH4)3VOF5, have been investigated by temperature-dependent infrared and Raman spectroscopy methods to determine the nature of phase transitions (PT) in these compounds. Dynamics of quasioctahedral groups was simulated within the framework of semi-empirical approach, which justified the cis-conformation of VO2F4(3-) (C2v) and the C4v geometry of VOF5(3-). The observed infrared and Raman spectra of both compounds at room temperature (RT) revealed the presence at least of two crystallographically independent octahedral groups...
January 4, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/28088027/an-alternative-strategy-to-western-blot-as-a-confirmatory-diagnostic-test-for-hiv-infection
#4
Xia Feng, Jibao Wang, Zhiyun Gao, Yu Tian, Ling Zhang, Huichao Chen, Tong Zhang, Lin Xiao, Jun Yao, Wenge Xing, Maofeng Qiu, Yan Jiang
BACKGROUND: In China, western blot (WB) is the recommended procedure for the diagnosis of HIV infection. However, this technique is time consuming and labor intensive, and its complexity restricts wide application in resource-limited regions. OBJECTIVE: The aim of this study was to evaluate the efficacy of a dry blood spots (DBS)-urine paired enzyme-linked immunosorbent assay (ELISA) test, instead of WB, for HIV antibody detection. STUDY DESIGN: Plasma, DBS, and urine samples were collected from 1213 subjects from different populations...
December 21, 2016: Journal of Clinical Virology: the Official Publication of the Pan American Society for Clinical Virology
https://www.readbyqxmd.com/read/28087951/a-phase-ii-study-of-concurrent-chemoradiotherapy-and-erlotinib-for-inoperable-esophageal-squamous-cell-carcinoma
#5
Chuanhua Zhao, Li Lin, Jianzhi Liu, Rongrui Liu, Yuling Chen, Feijiao Ge, Ru Jia, Yang Jin, Yan Wang, Jianming Xu
Cisplatin-based concurrent chemoradiotherapy for patients with unresectable, locally advanced esophageal squamous cell carcinoma (ESCC) is associated with significant toxicities that are often intolerable. Prognosis for this subgroup of patients remains poor, and new therapeutic approaches are urgently needed. We investigated the efficacy and safety of paclitaxel combined with erlotinib and concurrent radiotherapy in patients with inoperable ESCC. Erlotinib (150 mg) was administered daily for 60 days beginning at the start of radiotherapy, and paclitaxel (45 mg/m²) was administered weekly along with intensity modulated conformal radiotherapy (60 Gy in 30 fractions)...
August 30, 2016: Oncotarget
https://www.readbyqxmd.com/read/28087882/cooperatively-interlocked-2-1-type-%C3%AF-system-anion-complexes
#6
Ryohei Yamakado, Yukina Ashida, Ryuma Sato, Yasuteru Shigeta, Nobuhiro Yasuda, Hiromitsu Maeda
As fascinating examples of closely connected multiple π-electronic systems involving noncovalent interactions, the cooperatively interlocked [2+1]-type anion complexes of well-designed π-electronic molecules are reported. The anion-responsive π-electronic molecules investigated in this study are the boron complexes of dipyrrolyldiketones bearing arylethynyl moieties at the pyrrole α-positions. Diverse substituents were introduced at the terminal aryl moieties, thus controlling the cooperativity to form [2+1]-type complexes...
January 14, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28087737/a-homozygous-mutation-in-trim36-causes-autosomal-recessive-anencephaly-in-an-indian-family
#7
Nivedita Singh, Vishwanath Kumble Bhat, Ankana Tiwari, Srinivas G Kodaganur, Sagar J Tontanahal, Astha Sarda, K V Malini, Arun Kumar
Anencephaly is characterized by the absence of brain tissues and cranium. During primary neurulation stage of the embryo, the rostral part of the neural pore fails to close, leading to anencephaly. Anencephaly shows a heterogeneous etiology, ranging from environmental to genetic causes. The autosomal recessive inheritance of anencephaly has been reported in several populations. In this study, we employed whole-exome sequencing and identified a homozygous missense mutation c.1522C>A (p.Pro508Thr) in the TRIM36 gene as the cause of autosomal recessive anencephaly (APH) in an Indian family...
January 13, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28087691/imaging-proteins-at-the-single-molecule-level
#8
Jean-Nicolas Longchamp, Stephan Rauschenbach, Sabine Abb, Conrad Escher, Tatiana Latychevskaia, Klaus Kern, Hans-Werner Fink
Imaging single proteins has been a long-standing ambition for advancing various fields in natural science, as for instance structural biology, biophysics, and molecular nanotechnology. In particular, revealing the distinct conformations of an individual protein is of utmost importance. Here, we show the imaging of individual proteins and protein complexes by low-energy electron holography. Samples of individual proteins and protein complexes on ultraclean freestanding graphene were prepared by soft-landing electrospray ion beam deposition, which allows chemical- and conformational-specific selection and gentle deposition...
January 13, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28087578/distinct-binding-of-pet-ligands-pbb3-and-av-1451-to-tau-fibril-strains-in-neurodegenerative-tauopathies
#9
Maiko Ono, Naruhiko Sahara, Katsushi Kumata, Bin Ji, Ruiqing Ni, Shunsuke Koga, Dennis W Dickson, John Q Trojanowski, Virginia M-Y Lee, Mari Yoshida, Isao Hozumi, Yasumasa Yoshiyama, John C van Swieten, Agneta Nordberg, Tetsuya Suhara, Ming-Rong Zhang, Makoto Higuchi
Diverse neurodegenerative disorders are characterized by deposition of tau fibrils composed of conformers (i.e. strains) unique to each illness. The development of tau imaging agents has enabled visualization of tau lesions in tauopathy patients, but the modes of their binding to different tau strains remain elusive. Here we compared binding of tau positron emission tomography ligands, PBB3 and AV-1451, by fluorescence, autoradiography and homogenate binding assays with homologous and heterologous blockades using tauopathy brain samples...
January 12, 2017: Brain: a Journal of Neurology
https://www.readbyqxmd.com/read/28087374/what-stoichiometries-determined-by-mass-spectrometry-reveal-about-the-ligand-binding-mode-to-g-quadruplex-nucleic-acids
#10
Michael J Lecours, Adrien Marchand, Ahdia Anwar, Corinne Guetta, W Scott Hopkins, Valérie Gabelica
G-quadruplexes (G4s) have become important drug targets to regulate gene expression and telomere maintenance. Many studies on G4 ligand binding focus on determining the ligand binding affinities and selectivities. Ligands, however, can also affect the G4 conformation. Here we explain how to use electrospray ionization mass spectrometry (ESI-MS) to monitor simultaneously ligand binding and cation binding stoichiometries. The changes in potassium binding stoichiometry upon ligand binding hint at ligand-induced conformational changes involving a modification of the number of G-quartets...
January 10, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28087229/disease-associated-mutations-identify-a-novel-region-in-human-sting-necessary-for-the-control-of-type-i-interferon-signaling
#11
Isabelle Melki, Yoann Rose, Carolina Uggenti, Lien Van Eyck, Marie-Louise Frémond, Naoki Kitabayashi, Gillian I Rice, Emma M Jenkinson, Anaïs Boulai, Nadia Jeremiah, Marco Gattorno, Sefano Volpi, Olivero Sacco, Suzanne W J Terheggen-Lagro, Harm A W M Tiddens, Isabelle Meyts, Marie-Anne Morren, Petra De Haes, Carine Wouters, Eric Legius, Anniek Corveleyn, Frederic Rieux-Laucat, Christine Bodemer, Isabelle Callebaut, Mathieu P Rodero, Yanick J Crow
BACKGROUND: Gain-of-function mutations in transmembrane protein 173 (TMEM173) encoding stimulator of interferon genes (STING) underlie a recently described type I interferonopathy called STING-associated vasculopathy with onset in infancy (SAVI). OBJECTIVES: We sought to define the molecular and cellular pathology relating to 3 individuals variably exhibiting the core features of the SAVI phenotype including systemic inflammation, destructive skin lesions, and interstitial lung disease...
January 3, 2017: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/28086264/structural-insights-into-the-redox-sensing-mechanism-of-marr-type-regulator-abfr
#12
Guijie Liu, Xing Liu, Hongjiao Xu, Xichun Liu, Hu Zhou, Zhen Huang, Jianhua Gan, Hao Chen, Lefu Lan, Cai-Guang Yang
As a master redox-sensing MarR-family transcriptional regulator, AbfR participates in oxidative stress responses and virulence regulations in Staphylococcus epidermidis. Here, we present structural insights into the DNA-binding mechanism of AbfR in different oxidation states by determining the X-ray crystal structures of a reduced-AbfR/DNA complex, an overoxidized (Cys13-SO2H and Cys13-SO3H) AbfR/DNA, and 2-disulfide cross-linked AbfR dimer. Together with biochemical analyses, our results suggest that the redox regulation of AbfR-sensing displays two novel features: i) the reversible disulfide modification, but not the irreversible overoxidation, significantly abolishes the DNA-binding ability of the AbfR repressor; ii) either 1-disulfide cross-linked or 2-disulfide cross-linked AbfR dimer is biologically significant...
January 13, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28086263/observation-of-the-ring-puckering-vibrational-mode-in-thietane-cation
#13
Yu Ran Lee, Chung Bin Park, Jiye Hwang, Bongjune Sung, Hong Lae Kim, Chan Ho Kwon
We have measured the high-resolution vibrational spectra of a thietane (trimethylene sulfide) cation in the gas phase by employing the vacuum ultraviolet mass-analyzed threshold ionization (VUV-MATI) spectroscopic technique. Peaks in the low frequency region of the observed MATI spectrum of thietane originate from a progression of the ring puckering vibrational mode (typical in small heterocyclic molecules), which is successfully reproduced by quantum chemical calculations with one-dimensional (1D) symmetric double-well potentials along the ring puckering coordinates on both the S0 and D0 states, the ground electronic states of neutral and cation of thietane, respectively...
January 13, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28081463/analysis-of-the-results-of-recurrent-intracranial-meningiomas-treated-with-re-radiosurgery
#14
Moinay Kim, Do Hee Lee, Hyun Jung Kim Rn, Young Hyun Cho, Jeong Hoon Kim, Do Hoon Kwon
OBJECTS: Meningioma is the most common intracranial neoplasm, comprising approximately 30% of all primary intracranial tumors (Claus et al., 2005) [1]. Treatment options include observation, microsurgical resection, stereotactic radiosurgery (SRS), and whole brain radiation therapy (WBRT). Gamma knife radiosurgery (GKRS) is a very effective treatment for intracranial meningiomas; previous studies showed the tumor control rate at 5-10 years of follow-up as 84.3%-100% in all cases (Feigl et al...
December 29, 2016: Clinical Neurology and Neurosurgery
https://www.readbyqxmd.com/read/28081343/the-combined-effects-of-proteasome-inhibitor-bortezomib-with-topoisomerase-i-and-ii-inhibitors-on-topoisomerase-enzymes
#15
Emine Öksüzoğlu, Çiydem Tırınoğlu, Barış Kerimoğlu
BACKGROUND/AIM: DNA topoisomerases are ubiquitous enzymes that regulate conformational changes in DNA topology during essential cellular processes, and, for this reason, have been characterized as the cellular targets of a number of anticancer drugs. Bortezomib is a powerful proteasome inhibitor used in the treatment of hematological malignancies. In this study, we investigated the inhibitory effects of bortezomib on human topoisomerase I and II enzymes both alone and in combination modes with camptothecin and etoposide...
December 20, 2016: Turkish Journal of Medical Sciences
https://www.readbyqxmd.com/read/28081010/biological-dose-representation-for-carbon-ion-radiotherapy-of-unconventional-fractionation
#16
Nobuyuki Kanematsu, Taku Inaniwa
In carbon-ion radiotherapy, single-beam delivery each day in alternate directions has been common practice for efficient operation, taking advantage of the Bragg peak and the relative biological effectiveness (RBE) for uniform dose conformation to a tumor. Treatments are usually fractionated and treatment plans are evaluated with the total RBE-weighted dose; however, this is of limited relevance to the biological effect. In this study, we reformulate the biologically effective dose (BED) to normalize the dose-fractionation and cell-repopulation effects as well as the RBE of treating radiation, based on inactivation of a reference cell line by a reference carbon-ion radiation...
January 12, 2017: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/28080096/emotion-dysregulation-explains-associations-between-anxiety-sensitivity-and-hazardous-drinking-and-drinking-motives-among-adult-treatment-seeking-smokers
#17
Daniel J Paulus, Jaclyn Valadka, Michael S Businelle, Matthew W Gallagher, Andres G Viana, Norman B Schmidt, Michael J Zvolensky
Smoking and drinking frequently co-occur. For example, alcohol use is associated with smoking lapses during quit attempts. However, little is known regarding psychological factors explaining drinking among smokers. Anxiety sensitivity is a risk factor associated with hazardous drinking and drinking to cope and/or conform, although little is known about mechanisms underlying such associations. One potential explanatory factor is emotion dysregulation. The current study examined emotion dysregulation as an explanatory factor underlying Anxiety Sensitivity and 5 alcohol-related outcomes: hazardous drinking, alcohol consumption, alcohol problems, coping-oriented drinking, and drinking to conform...
January 12, 2017: Psychology of Addictive Behaviors: Journal of the Society of Psychologists in Addictive Behaviors
https://www.readbyqxmd.com/read/28080064/collective-excitations-in-protein-as-a-measure-of-balance-between-its-softness-and-rigidity
#18
Utsab Raj Shrestha, Debsindhu Bhowmik, Kurt William Van Delinder, Eugene Mamontov, Hugh M O'Neill, Qiu Zhang, Ahmet Alatas, Xiang-Qiang Chu
In this article, we elucidate the protein activity from the perspective of protein softness and flexibility by studying the collective phonon-like excitations in a globular protein, human serum albumin (HSA) and taking advantage of the state-of-the-art inelastic X-ray scattering (IXS) technique. Such excitations demonstrate that the protein becomes softer upon thermal denaturation due to disruption of weak non-covalent bonds. On the other hand, no significant change in the local excitations is detected in ligand- (drugs) bound HSA compared to the ligand-free HSA...
January 12, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28080057/identification-of-binding-modes-for-amino-naphthalene-2-cyanoacrylate-anca-probes-to-amyloid-fibrils-from-molecular-dynamics-simulations
#19
Huan He, Juan Xu, Dan-Yang Cheng, Li Fu, Yu-Shu Ge, Feng-Lei Jiang, Yi Liu
Amino naphthalene 2-Cyanoacrylate (ANCA) probe is a kind of fluorescent amyloid binding probe that can report a different fluorescence emission when bound to different types of amyloid deposits in tissue, while their interactions with amyloid fibrils remain unclear due to the insoluble nature of amyloid fibrils. Here, all atom molecular dynamics simulations were used to investigate the interaction between ANCA probes with three different amyloid fibrils. Two common binding modes of ANCA probes on Aβ40 amyloid fibrils were identified by cluster analysis of multiple simulations...
January 12, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28080056/metadynamics-simulations-distinguish-short-and-long-residence-time-inhibitors-of-cyclin-dependent-kinase-8
#20
Donatella Callegari, Alessio Lodola, Daniele Pala, Silvia Rivara, Marco Mor, Andrea Rizzi, Anna Maria Capelli
The duration of drug efficacy in vivo is a key aspect primarily addressed during the lead optimization phase of drug discovery. Hence, the availability of robust computational approaches that can predict the residence time of a compound at its target would accelerate candidate selection. Nowadays the theoretical prediction of this parameter is still very challenging. Starting from methods reported in the literature, we set up and validated a new metadynamics (META-D)-based protocol that was used to rank the experimental residence times of 10 arylpyrazole cyclin-dependent kinase 8 (CDK8) inhibitors for which target-bound X-ray structures are available...
January 12, 2017: Journal of Chemical Information and Modeling
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