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https://www.readbyqxmd.com/read/28687786/involvement-of-fancd2-in-energy-metabolism-via-atp5%C3%AE
#1
Panneerselvam Jayabal, Chi Ma, Manoj Nepal, Yihang Shen, Raymond Che, James Turkson, Peiwen Fei
Growing evidence supports a general hypothesis that aging and cancer are diseases related to energy metabolism. However, the involvement of Fanconi Anemia (FA) signaling, a unique genetic model system for studying human aging or cancer, in energy metabolism remains elusive. Here, we report that FA complementation group D2 protein (FANCD2) functionally impacts mitochondrial ATP production through its interaction with ATP5α, whereas this relationship was not observed in the mutant FANCD2 (K561R)-carrying cells...
July 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28681565/tubulin-acetylation-a-novel-functional-avenue-for-cdyl-in-sperm
#2
Sweta Parab, Veena Dalvi, Sushma Mylavaram, Abhipriya K, Susan Idicula-Thomas, Shobha Sonawane, Priyanka Parte
Motility in sperm is driven by the flagella, the principal component of which is the axoneme. The microtubules which make up the 9 + 2 axoneme are composed of heterodimers of alpha and beta tubulins and undergo several post-translational modifications. We have earlier reported that HDAC6 functions as tubulin deacetylase in sperm and has a role in sperm movement. While exploring the specific tubulin acetyltransferase (TAT) in sperm we observed the presence of Chromodomain Y-Like (CDYL), on the principal piece of rat spermatozoa which compelled us to explore its function in sperm...
July 6, 2017: Cytoskeleton
https://www.readbyqxmd.com/read/28671821/the-t-cell-receptor-can-bind-to-the-peptide-bound-major-histocompatibility-complex-and-uncomplexed-beta-2-microglobulin-through-distinct-binding-sites
#3
Patrick Sascha Merkle, Melita Irving, Song Hongjian, Mathias Ferber, Thomas J D Jørgensen, Kirsten Scholten, Immanuel Florian Luescher, George Coukos, Vincent Zoete, Michel A Cuendet, Olivier Michielin, Kasper D Rand
T-cell receptor (TCR)-mediated recognition of peptide-bound major histocompatibility complex (pMHC) initiates an adaptive immune response against antigen-presenting target cells. The recognition events take place at the TCR-pMHC interface and their implications on TCR conformation and dynamics are controversial. Here, we have measured the time-resolved hydrogen/deuterium exchange (HDX) of a soluble TCR in the presence and absence of its cognate pMHC by mass spectrometry to delineate the impact of pMHC binding on solution-phase structural dynamics in the TCR...
July 3, 2017: Biochemistry
https://www.readbyqxmd.com/read/28637675/structure-functional-aspects-of-the-human-riboflavin-transporter-3-slc52a3-role-of-the-predicted-glycosylation-and-substrate-interacting-sites
#4
Veedamali S Subramanian, Subrata Subai, Trevor Teafatiller, Jennifer A Bohl, Hamid M Said
The human riboflavin (RF) transporter-3 (hRFVT-3; product of the SLC52A3 gene) plays an essential role in the intestinal RF absorption process and is expressed exclusively at the apical membrane domain of polarized enterocytes. Previous studies have characterized different physiological/biological aspects of this transporter, but nothing is known about the glycosylation status of the hRFVT-3 protein and role of this modification in its physiology/biology. Additionally, little is known about the residues in the hRFVT-3 protein that interact with the ligand, RF...
June 21, 2017: American Journal of Physiology. Cell Physiology
https://www.readbyqxmd.com/read/28634712/site-directed-mutagenesis-under-the-direction-of-in-silico-protein-docking-modeling-reveals-the-active-site-residues-of-3-ketosteroid-%C3%AE-1-dehydrogenase-from-mycobacterium-neoaurum
#5
Ning Qin, Yanbing Shen, Xu Yang, Liqiu Su, Rui Tang, Wei Li, Min Wang
3-Ketosteroid-Δ(1)-dehydrogenases (KsdD) from Mycobacterium neoaurum could transform androst-4-ene-3,17-dione (AD) to androst-1,4-diene-3,17-dione. This reaction has a significant effect on the product of pharmaceutical steroid. The crystal structure and active site residues information of KsdD from Mycobacterium is not yet available, which result in the engineering of KsdD is tedious. In this study, by the way of protein modeling and site-directed mutagenesis, we find that, Y122, Y125, S138, E140 and Y541 from the FAD-binding domain and Y365 from the catalytic domain play a key role in this transformation...
July 2017: World Journal of Microbiology & Biotechnology
https://www.readbyqxmd.com/read/28596377/trowaglerix-venom-polypeptides-as-a-novel-antithrombotic-agent-by-targeting-immunoglobulin-like-domains-of-glycoprotein-vi-in-platelet
#6
Chien-Hsin Chang, Ching-Hu Chung, Yi-Shu Tu, Cheng-Chieh Tsai, Chun-Chieh Hsu, Hui-Chin Peng, Yufeng J Tseng, Tur-Fu Huang
OBJECTIVE: Currently prescribed antiplatelet drugs have 1 common side effect-an increased risk of hemorrhage and thrombocytopenia. On the contrary, bleeding defects associated with glycoprotein VI (GPVI) expression deficiency are usually slightly prolonged bleeding times. However, GPVI antagonists are lacking in clinic. APPROACH AND RESULTS: Using reverse-phase high-performance liquid chromatography and sequencing, we revealed the partial sequence of trowaglerix α subunit, a potent specific GPVI-targeting snaclec (snake venom C-type lectin protein)...
July 2017: Arteriosclerosis, Thrombosis, and Vascular Biology
https://www.readbyqxmd.com/read/28571840/staphylococcus-aureus-%C3%AE-toxin-in-aqueous-solution-behavior-in-monomeric-and-multimeric-states
#7
Maria Carolina de Araujo Melo, Cláudio Gabriel Rodrigues, Laercio Pol-Fachin
δ-Toxin is a 26 amino acid peptide capable of lysing several mammalian cell types and subcellular structures. Structurally, δ-toxin predominantly exhibits a α-helical secondary structure in membranes but, in aqueous solution, it adopts varying helical content. As no atomic-level data is available for this peptide in aqueous solutions and for the water-to-membrane transition, this work aims to characterize δ-toxin behavior in these conditions through molecular dynamics simulations in triplicates employing four different parameter sets...
August 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28544778/differential-regulation-of-protein-tyrosine-kinase-signalling-by-dock-and-the-ptp61f-variants
#8
Lee F Willoughby, Jan Manent, Kirsten Allan, Han Lee, Marta Portela, Florian Wiede, Coral Warr, Tzu-Ching Meng, Tony Tiganis, Helena E Richardson
Tyrosine phosphorylation-dependent signalling is coordinated by the opposing actions of protein tyrosine kinases (PTKs) and protein tyrosine phosphatases (PTPs). There is a growing list of adaptor proteins that interact with PTPs and facilitate the dephosphorylation of substrates. The extent to which any given adaptor confers selectivity for any given substrate in vivo remains unclear. Here we have taken advantage of Drosophila melanogaster as a model organism to explore the influence of the SH3/SH2 adaptor protein Dock on the abilities of the membrane (PTP61Fm)- and nuclear (PTP61Fn)-targeted variants of PTP61F (the Drosophila othologue of the mammalian enzymes PTP1B and TCPTP respectively) to repress PTK signalling pathways in vivo...
May 23, 2017: FEBS Journal
https://www.readbyqxmd.com/read/28541224/protein-protein-interaction-interface-residue-pair-prediction-based-on-deep-learning-architecture
#9
Zhenni Zhao, Xinqi Gong
MOTIVATION: Proteins usually fulfill their biological functions by interacting with other proteins. Although some methods have been developed to predict the binding sites of a monomer protein, these are not sufficient for prediction of the interaction between two monomer proteins. The correct prediction of interface residue pairs from two monomer proteins is still an open question and has great significance for practical experimental applications in the life sciences. We hope to build a method for the prediction of interface residue pairs that is suitable for those applications...
May 19, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28533339/structure-based-prediction-of-wnt-binding-affinities-for-frizzled-type-cysteine-rich-domains
#10
Mark Agostino, Sebastian Öther-Gee Pohl, Arun Dharmarajan
Wnt signaling pathways are of significant interest in development and oncogenesis. The first step in these pathways typically involves the binding of a Wnt protein to the cysteine-rich domain (CRD) of a Frizzled receptor. Wnt-Frizzled interactions can be antagonized by secreted Frizzled-related proteins (SFRPs), which also contain a Frizzled-like CRD. The large number of Wnts, Frizzleds, and SFRPs, as well as the hydrophobic nature of Wnt, poses challenges to laboratory-based investigations of interactions involving Wnt...
July 7, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28523927/retinoid-bms411-4-5-5-dimethyl-8-phenyl-5-6-dihydronaphthalen-2-yl-carbonyl-amino-benzoic-acid-a-potential-inhibitor-of-ns5a-protein-of-hepatitis-c-virus-a-candidate-for-combined-therapy-of-hepatitis-c-infection
#11
S Ibrahim, M J Asad, R T Mahmood, F H Wattoo, S Akhter, D Shahwar
Hepatitis C infection is a serious health issue worldwide caused by hepatitis C virus (HCV). There is an urgent need of search for new direct acting antiviral drugs due to the rapid development of drug resistance. The HCV NS5A protein is involved in creating resistance against antiviral therapy and there are also many reports that vitamin A deficiency is associated with non-responsiveness to antiviral treatment in HCV infected patients. So the present in silico study was aimed to find the relation between vitamin A deficiency and the NS5A protein's function in antiviral resistance...
2017: Acta Virologica
https://www.readbyqxmd.com/read/28510023/protein-rna-interactions-structural-biology-and-computational-modeling-techniques
#12
REVIEW
Susan Jones
RNA-binding proteins are functionally diverse within cells, being involved in RNA-metabolism, translation, DNA damage repair, and gene regulation at both the transcriptional and post-transcriptional levels. Much has been learnt about their interactions with RNAs through structure determination techniques and computational modeling. This review gives an overview of the structural data currently available for protein-RNA complexes, and discusses the technical issues facing structural biologists working to solve their structures...
December 2016: Biophysical Reviews
https://www.readbyqxmd.com/read/28505542/computational-modeling-of-protein-assemblies
#13
REVIEW
Neelesh Soni, M S Madhusudhan
Computational methods to predict the 3D structures of protein interactions fall into 3 categories-template based modeling, protein-protein docking and hybrid/integrative modeling. The two most important considerations for modeling methods are sampling and scoring conformations. Sampling has benefitted from techniques such as fast Fourier transforms (FFT), spherical harmonics and higher order manifolds. Scoring complexes to determine binding free energy is still a challenging problem. Rapid advances have been made in hybrid modeling where experimental data are amalgamated with computations...
May 12, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28500295/angiotensin-ii-type-1-adenosine-a-2a-receptor-oligomers-a-novel-target-for-tardive-dyskinesia
#14
Paulo A de Oliveira, James A R Dalton, Marc López-Cano, Adrià Ricarte, Xavier Morató, Filipe C Matheus, Andréia S Cunha, Christa E Müller, Reinaldo N Takahashi, Víctor Fernández-Dueñas, Jesús Giraldo, Rui D Prediger, Francisco Ciruela
Tardive dyskinesia (TD) is a serious motor side effect that may appear after long-term treatment with neuroleptics and mostly mediated by dopamine D2 receptors (D2Rs). Striatal D2R functioning may be finely regulated by either adenosine A2A receptor (A2AR) or angiotensin receptor type 1 (AT1R) through putative receptor heteromers. Here, we examined whether A2AR and AT1R may oligomerize in the striatum to synergistically modulate dopaminergic transmission. First, by using bioluminescence resonance energy transfer, we demonstrated a physical AT1R-A2AR interaction in cultured cells...
May 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28499419/across-proteome-modeling-of-dimer-structures-for-the-bottom-up-assembly-of-protein-protein-interaction-networks
#15
Surabhi Maheshwari, Michal Brylinski
BACKGROUND: Deciphering complete networks of interactions between proteins is the key to comprehend cellular regulatory mechanisms. A significant effort has been devoted to expanding the coverage of the proteome-wide interaction space at molecular level. Although a growing body of research shows that protein docking can, in principle, be used to predict biologically relevant interactions, the accuracy of the across-proteome identification of interacting partners and the selection of near-native complex structures still need to be improved...
May 12, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28486912/structural-investigation-of-vinca-domain-tubulin-binders-by-pharmacophore-atom-based-qsar-docking-and-molecular-dynamics-simulations
#16
Mohd Athar, Mohsin Yousuf Lone, Vijay M Khedkar, Ashish Radadiya, Anamik Shah, Prakash C Jha
Vinca domain of tubulin protein is a potent binding domain for various microtubule targeting drugs (MTD). However, binding mechanism and structure-activity-relationship (SAR) of this domain is not well understood in terms of ligand-receptor interactions and structure functionality requirements. Possibly, this limits the exploitation of this domain for developing novel clinical leads. Therefore, any step towards modelling and comprehension is of central contour. With this objective, we present here an In-silico insight through the development of a robust pharmacophore model and SAR analysis on a set of 26 well known Vinca domain binders of tubulin protein...
May 9, 2017: Combinatorial Chemistry & High Throughput Screening
https://www.readbyqxmd.com/read/28483642/structural-insights-into-the-molecular-function-of-human-2fe-2s-bola1-grx5-and-2fe-2s-bola3-grx5-complexes
#17
Veronica Nasta, Andrea Giachetti, Simone Ciofi-Baffoni, Lucia Banci
Members of the monothiol glutaredoxin family and members of the BolA-like protein family have recently emerged as specific interacting partners involved in iron-sulfur protein maturation and redox regulation pathways. It is known that human mitochondrial BOLA1 and BOLA3 form [2Fe-2S] cluster-bridged dimeric heterocomplexes with the monothiol glutaredoxin GRX5. The structure and cluster coordination of the two [2Fe-2S] heterocomplexes as well as their molecular function are, however, not defined yet. Experimentally-driven structural models of the two [2Fe-2S] cluster-bridged dimeric heterocomplexes, the relative stability of the two complexes and the redox properties of the [2Fe-2S] cluster bound to these complexes are here presented on the basis of UV/vis, CD, EPR and NMR spectroscopies and computational protein-protein docking...
August 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28467969/analysis-of-bos-taurus-and-sus-scrofa-x-and-y-chromosome-transcriptome-highlights-reproductive-driver-genes
#18
Faheem Ahmed Khan, Hui Liu, Hao Zhou, Kai Wang, Muhammad Tahir Ul Qamar, Nuruliarizki Shinta Pandupuspitasari, Zhang Shujun
The biology of sperm, its capability of fertilizing an egg and its role in sex ratio are the major biological questions in reproductive biology. To answer these question we integrated X and Y chromosome transcriptome across different species: Bos taurus and Sus scrofa and identified reproductive driver genes based on Weighted Gene Co-Expression Network Analysis (WGCNA) algorithm. Our strategy resulted in 11007 and 10445 unique genes consisting of 9 and 11 reproductive modules in Bos taurus and Sus scrofa, respectively...
April 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/28460116/the-pepattract-web-server-for-blind-large-scale-peptide-protein-docking
#19
Sjoerd J de Vries, Julien Rey, Christina E M Schindler, Martin Zacharias, Pierre Tuffery
Peptide-protein interactions are ubiquitous in the cell and form an important part of the interactome. Computational docking methods can complement experimental characterization of these complexes, but current protocols are not applicable on the proteome scale. pepATTRACT is a novel docking protocol that is fully blind, i.e. it does not require any information about the binding site. In various stages of its development, pepATTRACT has participated in CAPRI, making successful predictions for five out of seven protein-peptide targets...
April 29, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28430871/cluspro-peptidock-efficient-global-docking-of-peptide-recognition-motifs-using-fft
#20
Kathryn A Porter, Bing Xia, Dmitri Beglov, Tanggis Bohnuud, Nawsad Alam, Ora Schueler-Furman, Dima Kozakov
Summary: We present an approach for the efficient docking of peptide motifs to their free receptor structures. Using a motif based search, we can retrieve structural fragments from the Protein Data Bank (PDB) that are very similar to the peptide's final, bound conformation. We use a Fast Fourier Transform (FFT) based docking method to quickly perform global rigid body docking of these fragments to the receptor. According to CAPRI peptide docking criteria, an acceptable conformation can often be found among the top-ranking predictions...
April 18, 2017: Bioinformatics
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