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https://www.readbyqxmd.com/read/28343125/structural-modeling-of-human-organic-cation-transporters
#1
Tikam Chand Dakal, Rajender Kumar, Dindial Ramotar
Human organic cation transporters (hOCTs) belong to solute carriers (SLC) 22 family of membrane proteins that play a central role in transportation of chemotherapeutic drugs for several clinical and pathological conditions, including cancer and diabetes. These transporters mediate drug transport; however, the precise mechanism of drug-binding and transport by them is not fully uncovered yet, partly due to unavailability of any crystal structure record. In this work, we performed a multi-phasic approach to compute the 3D structural models of seven human organic cation transporters (hOCTs) starting from primary protein sequence...
March 18, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28339470/meiotic-recombination-modulates-the-structure-and-dynamics-of-the-synaptonemal-complex-during-c-elegans-meiosis
#2
Divya Pattabiraman, Baptiste Roelens, Alexander Woglar, Anne M Villeneuve
During meiotic prophase, a structure called the synaptonemal complex (SC) assembles at the interface between aligned pairs of homologous chromosomes, and crossover recombination events occur between their DNA molecules. Here we investigate the inter-relationships between these two hallmark features of the meiotic program in the nematode C. elegans, revealing dynamic properties of the SC that are modulated by recombination. We demonstrate that the SC incorporates new subunits and switches from a more highly dynamic/labile state to a more stable state as germ cells progress through the pachytene stage of meiotic prophase...
March 24, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28338992/identification-of-the-eucalyptus-grandis-chitinase-gene-family-and-expression-characterization-under-different-biotic-stress-challenges
#3
Peri A Tobias, Nanette Christie, Sanushka Naidoo, David I Guest, Carsten Külheim
Eucalyptus grandis (W. Hill ex Maiden) is an Australian Myrtaceae tree grown for timber in many parts of the world and for which the annotated genome sequence is available. Known to be susceptible to a number of pests and diseases, E. grandis is a useful study organism for investigating defense responses in woody plants. Chitinases are widespread in plants and cleave glycosidic bonds of chitin, the major structural component of fungal cell walls and arthropod exoskeletons. They are encoded by an important class of genes known to be up-regulated in plants in response to pathogens...
March 13, 2017: Tree Physiology
https://www.readbyqxmd.com/read/28336429/insight-into-stereochemistry-of-a-new-imp-allelic-variant-imp-55-metallo-%C3%AE-lactamase-identified-in-a-clinical-strain-of-acinetobacter-baumannii
#4
Mohammad Reza Shakibaie, Omid Azizi, Fereshteh Shahcheraghi
Metallo-β-lactamases (MBLs) such as IMPs are broad-spectrum β-lactamases that inactivate virtually all β-lactam antibiotics including carbapenems. In this study, we investigated the hydrolytic activity, phylogenetic relationship, three dimensional (3D) structure including zinc binding motif of a new IMP variant (IMP-55) identified in a clinical strain of Acinetobacter baumannii (AB). AB strain 56 was isolated from an adult ICU of a teaching hospital in Kerman, Iran. It exhibited MIC 32μg/ml to imipenem and showed MBL activity...
March 20, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28334019/cell-survival-and-differentiation-with-nanocrystalline-glass-like-carbon-using-substantia-nigra-dopaminergic-cells-derived-from-transgenic-mouse-embryos
#5
Noela Rodriguez-Losada, Pablo Romero, Guillermo Estivill-Torrús, Roberto Guzmán de Villoria, Jose A Aguirre
Regenerative medicine requires, in many cases, physical supports to facilitate appropriate cellular architecture, cell polarization and the improvement of the correct differentiation processes of embryonic stem cells, induced pluripotent cells or adult cells. Because the interest in carbon nanomaterials has grown within the last decade in light of a wide variety of applications, the aim of this study was to test and evaluate the suitability and cytocompatibility of a particular nanometer-thin nanocrystalline glass-like carbon film (NGLC) composed of curved graphene flakes joined by an amorphous carbon matrix...
2017: PloS One
https://www.readbyqxmd.com/read/28332978/structural-reorganization-of-the-chromatin-remodeling-enzyme-chd1-upon-engagement-with-nucleosomes
#6
Ramasubramanian Sundaramoorthy, Amanda L Hughes, Vijender Singh, Nicola Wiechens, Daniel P Ryan, Hassane El-Mkami, Maxim Petoukhov, Dmitri I Svergun, Barbara Treutlein, Salina Quack, Monika Fischer, Jens Michaelis, Bettina Böttcher, David G Norman, Tom Owen-Hughes
The yeast Chd1 protein acts to position nucleosomes across genomes. Here we model the structure of the Chd1 protein in solution and when bound to nucleosomes. In the apo state the DNA binding domain contacts the edge of the nucleosome while in the presence of the non-hydrolyzable ATP analog, ADP-beryllium fluoride, we observe additional interactions between the ATPase domain and the adjacent DNA gyre 1.5 helical turns from the dyad axis of symmetry. Binding in this conformation involves unravelling the outer turn of nucleosomal DNA and requires substantial reorientation of the DNA binding domain with respect to the ATPase domains...
March 23, 2017: ELife
https://www.readbyqxmd.com/read/28332759/structural-adaptation-of-a-protein-to-increased-metal-stress-nmr-structure-of-a-marine-snail-metallothionein-with-an-additional-domain
#7
Christian Baumann, Andrea Beil, Simon Jurt, Michael Niederwanger, Oscar Palacios, Mercè Capdevila, Sílvia Atrian, Reinhard Dallinger, Oliver Zerbe
In this study, we present an NMR structure of the metallothionein (MT) from the snail Littorina littorea (LlMT) in complex with Cd(2+) . LlMT is capable of binding 9 Zn(2+) or 9 Cd(2+) ions. Sequence alignments with other snail MTs revealed that the protein is likely composed of three domains. The study revealed that the protein is divided into three individual domains, each of which folds into a single well-defined three-metal cluster. The central α2 and C-terminal β domains are positioned with a unique relative orientation...
March 23, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28316759/fourier-analysis-of-conservation-patterns-in-protein-secondary-structure
#8
Ashok Palaniappan, Eric Jakobsson
Residue conservation is a common observation in alignments of protein families, underscoring positions important in protein structure and function. Though many methods measure the level of conservation of particular residue positions, currently we do not have a way to study spatial oscillations occurring in protein conservation patterns. It is known that hydrophobicity shows spatial oscillations in proteins, which is characterized by computing the hydrophobic moment of the protein domains. Here, we advance the study of moments of conservation of protein families to know whether there might exist spatial asymmetry in the conservation patterns of regular secondary structures...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28315995/ligand-based-virtual-screening-under-partial-shape-constraints
#9
Mathias M von Behren, Matthias Rarey
Ligand-based virtual screening has proven to be a viable technology during the search for new lead structures in drug discovery. Despite the rapidly increasing number of published methods, meaningful shape matching as well as ligand and target flexibility still remain open challenges. In this work, we analyze the influence of knowledge-based sterical constraints on the performance of the recently published ligand-based virtual screening method mRAISE. We introduce the concept of partial shape matching enabling a more differentiated view on chemical structure...
March 18, 2017: Journal of Computer-aided Molecular Design
https://www.readbyqxmd.com/read/28302170/identification-of-residues-important-for-the-activity-of-aldehyde-deformylating-oxygenase-through-investigation-into-the-structure-activity-relationship
#10
Qing Wang, Luyao Bao, Chenjun Jia, Mei Li, Jian-Jun Li, Xuefeng Lu
BACKGROUND: Aldehyde-deformylating oxygenase (ADO) is a key enzyme involved in the biosynthetic pathway of fatty alk(a/e)nes in cyanobacteria. However, cADO (cyanobacterial ADO) showed extreme low activity with the k cat value below 1 min(-1), which would limit its application in biofuel production. To identify the activity related key residues of cADO is urgently required. RESULTS: The amino acid residues which might affect cADO activity were identified based on the crystal structures and sequence alignment of cADOs, including the residues close to the di-iron center (Tyr39, Arg62, Gln110, Tyr122, Asp143 of cADO-1593), the protein surface (Trp 178 of cADO-1593), and those involved in two important hydrogen bonds (Gln49, Asn123 of cADO-1593, and Asp49, Asn123 of cADO-sll0208) and in the oligopeptide whose conformation changed in the absence of the di-iron center (Leu146, Asn149, Phe150 of cADO-1593, and Thr146, Leu148, Tyr150 of cADO-sll0208)...
March 16, 2017: BMC Biotechnology
https://www.readbyqxmd.com/read/28300777/functional-contributions-of-positive-charges-in-the-pore-lining-helix-3-of-the-bordetella-pertussis-cyaa-hemolysin-to-hemolytic-activity-and-ion-channel-opening
#11
Chattip Kurehong, Chalermpol Kanchanawarin, Busaba Powthongchin, Panchika Prangkio, Gerd Katzenmeier, Chanan Angsuthanasombat
The Bordetella pertussis CyaA-hemolysin (CyaA-Hly) domain was previously demonstrated to be an important determinant for hemolysis against target erythrocytes and ion-channel formation in planar lipid bilayers (PLBs). Here, net-charge variations in the pore-lining helix of thirteen related RTX cytolysins including CyaA-Hly were revealed by amino acid sequence alignments, reflecting their different degrees of hemolytic activity. To analyze possible functional effects of net-charge alterations on hemolytic activity and channel formation of CyaA-Hly, specific mutations were made at Gln(574) or Glu(581) in its pore-lining α3 of which both residues are highly conserved Lys in the three highly active RTX cytolysins (i...
March 16, 2017: Toxins
https://www.readbyqxmd.com/read/28296389/abrogated-cell-contact-guidance-on-amino-functionalized-microgrooves
#12
Caroline Mörke, Henrike Rebl, Birgit Finke, Manuela Dubs, Peter Nestler, Aissam Airoudj, Vincent Roucoules, Matthias Schnabelrauch, Andreas Körtge, Karine Anselme, Christiane A Helm, J Barbara Nebe
Topographical and chemical features of biomaterial surfaces affect the cell physiology at the interface and are promising tools for the improvement of implants. The dominance of the surface topography on cell behavior is often accentuated. Striated surfaces induce an alignment of cells and their intracellular adhesion-mediated components. Recently, it could be demonstrated that a chemical modification via plasma polymerized allylamine was not only able to boost osteoblast cell adhesion and spreading but also override the cell alignment on stochastically machined titanium...
March 15, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28291352/understanding-the-molecular-determinant-of-reversible-human-monoamine-oxidase-b-inhibitors-containing-2h-chromen-2-one-core-structure-based-and-ligand-based-derived-3-d-qsar-predictive-models
#13
Milan Mladenovic, Alexandros Patsilinakos, Adele Pirolli, Manuela Sabatino, Rino Ragno
Monoamine oxidase B (MAO B) catalyzes the oxidative deamination of aryalkylamines neurotransmitters with concomitant reduction of oxygen to hydrogen peroxide. Consequently, the enzyme's malfunction can induce oxidative damage to mitochondrial DNA and mediates development of Parkinson's disease. Thus, MAO B emerges as a promising target for developing pharmaceuticals potentially useful to treat this vicious neurodegenerative condition. Aiming to contribute to the development of drugs with the reversible mechanism of MAO B inhibition only, herein, an extended in silico-in vitro procedure for the selection of novel MAO B inhibitors is demonstrated, including: (1) definition of optimized and validated structure-based (SB) 3-D QSAR models derived from available co-crystallized inhibitor-MAO B complexes; (2) elaboration of structure-activity relationships (SAR) features for either irreversible or reversible MAO B inhibitors to characterize and improve coumarin-based inhibitor activity (Protein Data Bank ID: 2V61) as the most potent reversible lead compound; (3) definition of structure-based (SB) and ligand-based (LB) alignment rules assessments by which virtually any untested potential MAO B inhibitor might be evaluated; (4) predictive ability validation of the best 3-D QSAR model through SB/LB modeling of four coumarin-based external test sets (267 compounds); (5) design and SB/LB alignment of novel coumarin-based scaffolds experimentally validated through synthesis and biological evaluation in vitro...
March 14, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28282119/patchsearch-a-fast-computational-method-for-off-target-detection
#14
Inès Rasolohery, Gautier Moroy, Frédéric Guyon
Many therapeutic molecules are known to bind several proteins, which can be different from the initially targeted one. Such unexpected interactions with proteins called off-targets can lead to adverse effects. Potential off-target identification is important to predict to avoid drug side effects or to discover new targets for existing drugs. We propose a new program named PatchSearch that implements local nonsequential searching for similar binding sites on protein surfaces with a controlled amount of flexibility...
March 24, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28281259/hypermulticolor-detector-for-quantum-antibody-based-concurrent-detection-of-intracellular-markers-for-hiv-diagnosis
#15
Annie Agnes Suganya Samson, Joon Myong Song
Antiretroviral treatment can reduce the death rate of human immunodeficiency virus (HIV) infection, and its effectiveness is maximized at the early stage of HIV infection. The present protocol demonstrates an early stage high-content HIV diagnosis based on multicolor concurrent monitoring of CD4, CD8, and CD3 coreceptors and F-actin cytoskeleton using quantum dot (Qdot)-antibody conjugates at the single cell level. Artificial HIV infection of peripheral blood mononuclear cells (PBMCs) can be achieved by treating PBMCs with gp120...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28279821/targeting-the-dengue-%C3%AE-og-with-serotype-specific-alkaloid-virtual-leads
#16
Aditi Gangopadhyay, Hirak Jyoti Chakraborty, Abhijit Datta
The dengue envelope β-OG pocket is a crucial hinge for mediating virus-host fusion via conformational changes in the envelope to the fusion-competent form. The β-OG pocket is a small molecule target site for inhibition of virus-host fusion. As of date, the only structure of the β-OG pocket known is of serotype 2. Studies of β-OG inhibition by small molecules primarily target viral serotype 2. Envelope and β-OG sequence alignments, reveal dissimilarities across serotypes. In light of protein sequence-structure-function correlation, sequence variations suggest serotypic variations in β-OG druggability...
March 1, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28279793/identification-and-characterization-of-a-novel-conserved-46-kd-maltoporin-of-aeromonas-hydrophila-as-a-versatile-vaccine-candidate-in-european-eel-anguilla-anguilla
#17
Jianjun Feng, Peng Lin, Songlin Guo, Yuanyuan Jia, Yilei Wang, Frank Zadlock, Ziping Zhang
European eel (Anguilla anguilla) is a crucial economic fish that has been plagued by Aeromonas hydrophila infections for many years. Vaccines that are cross-protective against multiple serotypes could provide an effective control against A. hydrophila-mediated diseases. The outer membrane proteins (OMPs) are highly immunogenic and capable of eliciting protective immune responses. This study reports the identification of a novel 46 kD maltoporin that is a conserved protective antigen for different serotypes of A...
March 6, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28277940/a-single-structurally-conserved-sumoylation-site-in-crmp2-controls-nav1-7-function
#18
Erik Thomas Dustrude, Samantha Perez-Miller, Liberty François-Moutal, Aubin Moutal, May Khanna, Rajesh Khanna
The neuronal collapsin response mediator protein 2 (CRMP2) undergoes several posttranslational modifications that codify its functions. Most recently, CRMP2 SUMOylation (addition of small ubiquitin like modifier (SUMO)) was identified as a key regulatory step within a modification program that codes for CRMP2 interaction with, and trafficking of, voltage-gated sodium channel NaV1.7. In this paper, we illustrate the utility of combining sequence alignment within protein families with structural analysis to identify, from several putative SUMOylation sites, those that are most likely to be biologically relevant...
February 28, 2017: Channels
https://www.readbyqxmd.com/read/28274174/samira-vp-a-simple-protein-alignment-method-with-rechecking-the-alphabet-vector-positions
#19
Samira Fotoohifiroozabadi, Mohd Saberi Mohamad, Safaai Deris
Protein structure alignment and comparisons that are based on an alphabetical demonstration of protein structure are more simple to run with faster evaluation processes; thus, their accuracy is not as reliable as three-dimension (3D)-based tools. As a 1D method candidate, TS-AMIR used the alphabetic demonstration of secondary-structure elements (SSE) of proteins and compared the assigned letters to each SSE using the [Formula: see text]-gram method. Although the results were comparable to those obtained via geometrical methods, the SSE length and accuracy of adjacency between SSEs were not considered in the comparison process...
January 26, 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28265494/purification-and-biochemical-characterization-of-recombinant-persicaria-minor%C3%A2-%C3%AE-sesquiphellandrene-synthase
#20
De-Sheng Ker, Sze Lei Pang, Noor Farhan Othman, Sekar Kumaran, Ee Fun Tan, Thiba Krishnan, Kok Gan Chan, Roohaida Othman, Maizom Hassan, Chyan Leong Ng
BACKGROUND: Sesquiterpenes are 15-carbon terpenes synthesized by sesquiterpene synthases using farnesyl diphosphate (FPP) as a substrate. Recently, a sesquiterpene synthase gene that encodes a 65 kDa protein was isolated from the aromatic plant Persicaria minor. Here, we report the expression, purification and characterization of recombinant P. minor sesquiterpene synthase protein (PmSTS). Insights into the catalytic active site were further provided by structural analysis guided by multiple sequence alignment...
2017: PeerJ
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