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https://www.readbyqxmd.com/read/28903352/analysis-of-bos-taurus-and-sus-scrofa-x-and-y-chromosome-transcriptome-highlights-reproductive-driver-genes
#1
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...
August 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28891124/dockground-a-comprehensive-data-resource-for-modeling-of-protein-complexes
#2
Petras J Kundrotas, Ivan Anishchenko, Taras Dauzhenka, Ian Kotthoff, Daniil Mnevets, Matthew M Copeland, Ilya A Vakser
Characterization of life processes at the molecular level requires structural details of protein interactions. The number of experimentally determined structures of protein-protein complexes accounts only for a fraction of known protein interactions. This gap in structural description of the interactome has to be bridged by modeling. An essential part of the development of structural modeling/docking techniques for protein interactions is databases of protein-protein complexes. They are necessary for studying protein interfaces, providing a knowledge base for docking algorithms, developing intermolecular potentials, search procedures, and scoring functions...
September 10, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28888036/exploring-the-interaction-between-mycobacterium-tuberculosisenolase-and-human-plasminogen-using-computational-methods-and-experimental-techniques
#3
Amit Rahi, Alisha Dhiman, Damini Singh, Andrew M Lynn, Mohd Rehan, Rakesh Bhatnagar
Surface localized microbial enolases' binding with human plasminogen has been increasingly proven to have an important role in initial infection cycle of several human pathogens.Likewise, surface localized Mycobacterium tuberculosis (Mtb) enolase also binds to human plasminogen, and this interaction may entail crucial consequences for granuloma stability. The current study is the first attempt to explore the plasminogen interacting residues of enolase from Mtb. Beginning with the structural modeling of Mtbenolase, the binding pose of Mtbenolase and human plasminogen was predicted using protein-protein docking simulations...
September 9, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28881968/snapdock-template-based-docking-by-geometric-hashing
#4
Michael Estrin, Haim J Wolfson
Motivation: A highly efficient template-based protein-protein docking algorithm, nicknamed SnapDock, is presented. It employs a Geometric Hashing-based structural alignment scheme to align the target proteins to the interfaces of non-redundant protein-protein interface libraries. Docking of a pair of proteins utilizing the 22 600 interface PIFACE library is performed in < 2 min on the average. A flexible version of the algorithm allowing hinge motion in one of the proteins is presented as well...
July 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28868119/coumarin-derivatives-bearing-benzoheterocycle-moiety-synthesis-cholinesterase-inhibitory-and-docking-simulation-study
#5
Kimia Hirbod, Leili Jalili-Baleh, Hamid Nadri, Seyed Esmaeil Sadat Ebrahimi, Alireza Moradi, Bahar Pakseresht, Alireza Foroumadi, Abbas Shafiee, Mehdi Khoobi
OBJECTIVES: To investigate the efficiency of a novel series of coumarin derivatives bearing benzoheterocycle moiety as novel cholinesterase inhibitors. MATERIALS AND METHODS: Different 7-hydroxycoumarin derivatives were synthesized via Pechmann or Knoevenagel condensation and conjugated to different benzoheterocycle (8-hydroxyquinoline, 2-mercaptobenzoxazole or 2-mercaptobenzimidazole) using dibromoalkanes 3a-m: Final compounds were evaluated against acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) by Ellman's method...
June 2017: Iranian Journal of Basic Medical Sciences
https://www.readbyqxmd.com/read/28845596/improved-performance-in-capri-round-37-using-lzerd-docking-and-template-based-modeling-with-combined-scoring-functions
#6
Lenna X Peterson, Woong-Hee Shin, Hyungrae Kim, Daisuke Kihara
We report our group's performance for protein-protein complex structure prediction and scoring in Round 37 of the Critical Assessment of PRediction of Interactions (CAPRI), an objective assessment of protein-protein complex modeling. We demonstrated noticeable improvement in both prediction and scoring compared to previous rounds of CAPRI, with our human predictor group near the top of the rankings and our server scorer group at the top. This is the first time in CAPRI that a server has been the top scorer group...
August 28, 2017: Proteins
https://www.readbyqxmd.com/read/28841721/docking-based-modeling-of-protein-protein-interfaces-for-extensive-structural-and-functional-characterization-of-missense-mutations
#7
Didier Barradas-Bautista, Juan Fernández-Recio
Next-generation sequencing (NGS) technologies are providing genomic information for an increasing number of healthy individuals and patient populations. In the context of the large amount of generated genomic data that is being generated, understanding the effect of disease-related mutations at molecular level can contribute to close the gap between genotype and phenotype and thus improve prevention, diagnosis or treatment of a pathological condition. In order to fully characterize the effect of a pathological mutation and have useful information for prediction purposes, it is important first to identify whether the mutation is located at a protein-binding interface, and second to understand the effect on the binding affinity of the affected interaction/s...
2017: PloS One
https://www.readbyqxmd.com/read/28840418/combining-self-and-cross-docking-as-benchmark-tools-the-performance-of-dockbench-in-the-d3r-grand-challenge-2
#8
Veronica Salmaso, Mattia Sturlese, Alberto Cuzzolin, Stefano Moro
Molecular docking is a powerful tool in the field of computer-aided molecular design. In particular, it is the technique of choice for the prediction of a ligand pose within its target binding site. A multitude of docking methods is available nowadays, whose performance may vary depending on the data set. Therefore, some non-trivial choices should be made before starting a docking simulation. In the same framework, the selection of the target structure to use could be challenging, since the number of available experimental structures is increasing...
August 24, 2017: Journal of Computer-aided Molecular Design
https://www.readbyqxmd.com/read/28830442/modeling-ephb4-ephrinb2-protein-protein-interaction-using-flexible-docking-of-a-short-linear-motif
#9
Maciej Pawel Ciemny, Mateusz Kurcinski, Maciej Blaszczyk, Andrzej Kolinski, Sebastian Kmiecik
BACKGROUND: Many protein-protein interactions are mediated by a short linear motif. Usually, amino acid sequences of those motifs are known or can be predicted. It is much harder to experimentally characterize or predict their structure in the bound form. In this work, we test a possibility of using flexible docking of a short linear motif to predict the interaction interface of the EphB4-EphrinB2 complex (a system extensively studied for its significance in tumor progression). METHODS: In the modeling, we only use knowledge about the motif sequence and experimental structures of EphB4-EphrinB2 complex partners...
August 18, 2017: Biomedical Engineering Online
https://www.readbyqxmd.com/read/28780192/a-novel-hpv-prophylactic-peptide-vaccine-designed-by-immunoinformatics-and-structural-vaccinology-approaches
#10
Manica Negahdaripour, Mahboobeh Eslami, Navid Nezafat, Nasim Hajighahramani, Mohammad Bagher Ghoshoon, Eskandar Shoolian, Ali Dehshahri, Nasrollah Erfani, Mohammad Hossein Morowvat, Younes Ghasemi
Human papillomavirus (HPV)-caused cervical cancer is the fourth common female cancer globally. Despite availability of three effective vaccines in market, development of HPV prophylactic vaccines is still pursued due to affordability issues and type-restricted protection of the marketed vaccines. Investigational second generation prophylactic HPV vaccines are mostly exploiting epitopes from the virus minor capsid protein (L2), which despite many advantages suffer from low immunogenicity, a common problem of epitope vaccines...
August 2, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28775330/enriching-traditional-protein-protein-interaction-networks-with-alternative-conformations-of-proteins
#11
Farideh Halakou, Emel Sen Kilic, Engin Cukuroglu, Ozlem Keskin, Attila Gursoy
Traditional Protein-Protein Interaction (PPI) networks, which use a node and edge representation, lack some valuable information about the mechanistic details of biological processes. Mapping protein structures to these PPI networks not only provides structural details of each interaction but also helps us to find the mutual exclusive interactions. Yet it is not a comprehensive representation as it neglects the conformational changes of proteins which may lead to different interactions, functions, and downstream signalling...
August 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28687786/involvement-of-fancd2-in-energy-metabolism-via-atp5%C3%AE
#12
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
#13
Sweta Parab, Veena Dalvi, Sushma Mylavaram, Abhipriya Kishore, 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-%C3%AE-2-microglobulin-through-distinct-binding-sites
#14
Patrick S Merkle, Melita Irving, Song Hongjian, Mathias Ferber, Thomas J D Jørgensen, Kirsten Scholten, Immanuel Luescher, George Coukos, Vincent Zoete, Michel A Cuendet, Olivier Michielin, Kasper D Rand
T-Cell receptor (TCR)-mediated recognition of the 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 effects 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...
August 1, 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
#15
Veedamali S Subramanian, Subrata Sabui, 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...
August 1, 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
#16
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
#17
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
#18
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
#19
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
#20
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
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