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"protein docking"

Kazuhiro Takemura, Nobuyuki Matubayasi, Akio Kitao
To aid the evaluation of protein-protein complex model structures generated by protein docking prediction (decoys), we previously developed a method to calculate the binding free energies for complexes. The method combines a short (2 ns) all-atom molecular dynamics simulation with explicit solvent and solution theory in the energy representation (ER). We showed that this method successfully selected structures similar to the native complex structure (near-native decoys) as the lowest binding free energy structures...
March 14, 2018: Journal of Chemical Physics
Nika Abdollahi, Alexandre Albani, Eric Anthony, Agnes Baud, Mélissa Cardon, Robert Clerc, Dariusz Czernecki, Romain Conte, Laurent David, Agathe Delaune, Samia Djerroud, Pauline Fourgoux, Nadège Guiglielmoni, Jeanne Laurentie, Nathalie Lehmann, Camille Lochard, Rémi Montagne, Vasiliki Myrodia, Vaitea Opuu, Elise Parey, Lélia Polit, Sylvain Privé, Chloé Quignot, Maria Ruiz-Cuevas, Mariam Sissoko, Nicolas Sompairac, Audrey Vallerix, Violaine Verrecchia, Marc Delarue, Raphael Guérois, Yann Ponty, Sophie Sacquin-Mora, Alessandra Carbone, Christine Froidevaux, Stéphane Le Crom, Olivier Lespinet, Martin Weigt, Samer Abboud, Juliana Bernardes, Guillaume Bouvier, Chloé Dequeker, Arnaud Ferré, Patrick Fuchs, Gaëlle Lelandais, Pierre Poulain, Hugues Richard, Hugo Schweke, Elodie Laine, Anne Lopes
We present a new educational initiative called Meet-U that aims to train students for collaborative work in computational biology and to bridge the gap between education and research. Meet-U mimics the setup of collaborative research projects and takes advantage of the most popular tools for collaborative work and of cloud computing. Students are grouped in teams of 4-5 people and have to realize a project from A to Z that answers a challenging question in biology. Meet-U promotes "coopetition," as the students collaborate within and across the teams and are also in competition with each other to develop the best final product...
March 2018: PLoS Computational Biology
Paula G Slater, Sebastian E Gutierrez-Maldonado, Katia Gysling, Carlos F Lagos
The corticotropin-releasing factor (CRF) system is a key mediator of the stress response and addictive behavior. The CRF system includes four peptides: The CRF system includes four peptides: CRF, urocortins I-III, CRF binding protein (CRF-BP) that binds CRF with high affinity, and two class B G-protein coupled receptors CRF1 R and CRF2 R. CRF-BP is a secreted protein without significant sequence homology to CRF receptors or to any other known class of protein. Recently, it has been described a potentiation role of CRF-BP over CRF signaling through CRF2 R in addictive-related neuronal plasticity and behavior...
2018: Frontiers in Endocrinology
Salvatore Condello, Livia Elena Sima, Cristina Ivan, Horacio Cardenas, Gary E Schiltz, Rama K Mishra, Daniela Matei
Cancer progression and recurrence are linked to a rare population of cancer stem cells (CSC). Here we hypothesized that interactions with the extracellular matrix drive CSC proliferation and tumor-initiating capacity and investigated the functions of scaffold protein tissue transglutaminase (TG2) in ovarian CSC. Complexes formed by TG2, fibronectin (FN), and integrin β1 were enriched in ovarian CSC and detectable in tumors. A function-inhibiting antibody against the TG2 FN-binding domain suppressed complex formation, CSC proliferation as spheroids, tumor-initiating capacity, and stemness-associated Wnt/β-catenin signaling...
March 6, 2018: Cancer Research
Varsha D Badal, Petras J Kundrotas, Ilya A Vakser
BACKGROUND: Structural modeling of protein-protein interactions produces a large number of putative configurations of the protein complexes. Identification of the near-native models among them is a serious challenge. Publicly available results of biomedical research may provide constraints on the binding mode, which can be essential for the docking. Our text-mining (TM) tool, which extracts binding site residues from the PubMed abstracts, was successfully applied to protein docking (Badal et al...
March 5, 2018: BMC Bioinformatics
Pawan Kumar Raghav, Ajay Kumar Singh, Gurudutta Gangenahalli
Several signaling pathways, ligands, and genes that regulate proliferative and self-renewal properties of the Hematopoietic Stem Cells (HSCs) have been studied meticulously. One of the signaling pathways that play a crucial role in the process of hematopoiesis is the Stem Cell Factor (SCF) mediated c-Kit pathway. The c-Kit is a Receptor Tyrosine Kinase (RTK), which is expressed in the cells including HSCs. It undergoes dimerization upon binding with its cognate ligand SCF. As a result, phosphorylation of the Juxtamembrane (JM) domain of c-Kit takes place at Tyr568 and Tyr570 residues...
February 17, 2018: Mutation Research
Adel Aloraini, Karim M ElSawy
Understanding gene-gene interaction and its causal relationship to protein-protein interaction is a viable route for understanding drug action at the genetic level, which is largely hindered by inability to robustly map gene regulatory networks. Here, we use biological prior knowledge of family-to-family gene interactions available in the KEGG database to reveal individual gene-to-gene interaction networks that underlie the gene expression profiles of 2 cell line data sets, sensitive and resistive to neoadjuvant docetaxel breast anticancer drug...
2018: Cancer Informatics
Ming Hong, Honghui Cheng, Lei Song, Wencai Wang, Qi Wang, Donggang Xu, Weiwei Xing
As one of the major active ingredients in Radix Scutellariae, wogonin has been shown to be associated with various pharmacological activities on cancer cell growth, apoptosis, and cell invasion and migration. Here, we demonstrated that wogonin may harbor potential anti-metastatic activities in hepatocarcinoma (HCC). The anti-metastasis potential of wogonin and its underlying mechanisms were evaluated by ligand-protein docking approach, surface plasmon resonance assay, and in vitro gelatin zymography studies...
February 11, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Mahesh Chandra Patra, Sangdun Choi
The toll/interleukin 1 receptor (TIR) domain-containing adaptor protein (TIRAP) plays an important role in the toll-like receptor (TLR) 2, TLR4, TLR7, and TLR9 signaling pathways. TIRAP anchors to phosphatidylinositol (PI) 4,5-bisphosphate (PIP2) on the plasma membrane and PI (3,4,5)-trisphosphate (PIP3) on the endosomal membrane and assists in recruitment of the myeloid differentiation primary response 88 protein to activated TLRs. To date, the structure and mechanism of TIRAP's membrane association are only partially understood...
2018: Frontiers in Immunology
Sebastian Daberdaku, Carlo Ferrari
BACKGROUND: The correct determination of protein-protein interaction interfaces is important for understanding disease mechanisms and for rational drug design. To date, several computational methods for the prediction of protein interfaces have been developed, but the interface prediction problem is still not fully understood. Experimental evidence suggests that the location of binding sites is imprinted in the protein structure, but there are major differences among the interfaces of the various protein types: the characterising properties can vary a lot depending on the interaction type and function...
February 6, 2018: BMC Bioinformatics
Ankur Chaudhuri, Sampa Biswas, Sibani Chakraborty
Meprins are a group of zinc metalloproteases of the astacin family which play pivotal role in several physiological and pathologocal diseases. The inhibition of the meprins by various inhibitors; macromolecular and small molecules are crucial in the control of several diseases. Human cystatinC, an amyloidogenic protein is reported to be an endogenous inhibitor of meprin-α. In this computational study, we elucidate a rational model for meprinα-cystatinC complex by using protein-protein docking. The complex model as well as the unbound form was evaluated by molecular dynamics simulation...
January 17, 2018: Journal of Biomolecular Structure & Dynamics
Lenna X Peterson, Yoichiro Togawa, Juan Esquivel-Rodriguez, Genki Terashi, Charles Christoffer, Amitava Roy, Woong-Hee Shin, Daisuke Kihara
Protein-protein interactions are the cornerstone of numerous biological processes. Although an increasing number of protein complex structures have been determined using experimental methods, relatively fewer studies have been performed to determine the assembly order of complexes. In addition to the insights into the molecular mechanisms of biological function provided by the structure of a complex, knowing the assembly order is important for understanding the process of complex formation. Assembly order is also practically useful for constructing subcomplexes as a step toward solving the entire complex experimentally, designing artificial protein complexes, and developing drugs that interrupt a critical step in the complex assembly...
January 2018: PLoS Computational Biology
Masato Hoshi, Antoine Reginensi, Matthew S Joens, James A J Fitzpatrick, Helen McNeill, Sanjay Jain
The epithelial Wolffian duct (WD) inserts into the cloaca (primitive bladder) before metanephric kidney development, thereby establishing the initial plumbing for eventual joining of the ureters and bladder. Defects in this process cause common anomalies in the spectrum of congenital anomalies of the kidney and urinary tract (CAKUT). However, developmental, cellular, and molecular mechanisms of WD-cloaca fusion are poorly understood. Through systematic analysis of early WD tip development in mice, we discovered that a novel process of spatiotemporally regulated apoptosis in WD and cloaca was necessary for WD-cloaca fusion...
January 11, 2018: Journal of the American Society of Nephrology: JASN
Qiuying Yu, Fangyu Wang, Xiaofei Hu, Guangxu Xing, Ruiguang Deng, Junqing Guo, Anchun Cheng, Jing Wang, Junfang Hao, Dong Zhao, Man Teng, Gaiping Zhang
BACKGROUND: Based on the importance of peptides in regulatory interactions, peptide-protein docking has attracted many researchers' attention. Currently, a variety of methods specialized for molecular modeling of peptide-protein docking such as local search and global search are implemented. RESULTS: In this work, the interactions of eleven peptides and CSFV E2 protein were evaluated by GalaxyPepDock and FlexX/ SYBYL program, respectively. Then, the assessment scores of all the peptides were conducted a correlation analysis with their KD values...
January 9, 2018: Journal of the Science of Food and Agriculture
Abinaya Balasubramanian, Manish Bhattacharjee, Meenakumari Sakthivel, Munusamy Thirumavalavan, Thirumurthy Madhavan, Santhosh Kumar Nagarajan, Velusamy Palaniyandi, Pachaiappan Raman
As the aim of this present study, a proteinaceous α-amylase inhibitor has been isolated from the rhizome of Cheilocostus specious (C. speciosus) and was purified using DEAE cellulose anion exchange chromatography followed by gel filtration using Sephacryl-S-200 column. The purity and molecular mass of the purified inhibitor was determined by SDS-PAGE and LC-MS respectively. The molecular mass of the purified inhibitor was determined to be 31.18kDa. Protein-protein docking was also carried out as molecular model...
January 2, 2018: International Journal of Biological Macromolecules
Vytautas Raškevičius, Vaidas Jotautis, Lina Rimkutė, Alina Marandykina, Mintautė Kazokaitė, Visvaldas Kairys, Vytenis Arvydas Skeberdis
In our recent study, we have demonstrated that short carbon chain n -alcohols (up to octanol) stimulated while long carbon chain n -alcohols inhibited the conductance of connexin 36 (Cx36) gap junction (GJ) channels. In contrast, GJ channels composed of other types of Cxs all were inhibited by n -alcohols independently on their carbon chain length. To identify the putative structural domains of Cx36, responsible for the dual effect of n -alcohols, we performed structural modeling of Cx36 protein docking with hexanol and isoflurane that stimulated as well as nonanol and carbenoxolone that inhibited the conductance of Cx36 GJs and revealed their multiple common docking sites and a single pocket accessible only to hexanol and isoflurane...
January 3, 2018: Bioscience Reports
Lili Li, Juan Xu, Guohua Qiu, Jianming Ying, Zhenfang Du, Tingxiu Xiang, Kai Yau Wong, Gopesh Srivastava, Xiao-Feng Zhu, Tony S Mok, Anthony Tc Chan, Francis Kl Chan, Richard F Ambinder, Qian Tao
Rationale: Oncogenic STAT3 signaling activation and 3p22-21.3 locus alteration are common in multiple tumors, especially carcinomas of the nasopharynx, esophagus and lung. Whether these two events are linked remains unclear. Our CpG methylome analysis identified a 3p22.2 gene, DLEC1, as a methylated target in esophageal squamous cell (ESCC), nasopharyngeal (NPC) and lung carcinomas. Thus, we further characterized its epigenetic abnormalities and functions. Methods: CpG methylomes were established by methylated DNA immunoprecipitation...
2018: Theranostics
Ting Feng, Fu Chen, Yu Kang, Huiyong Sun, Hui Liu, Dan Li, Feng Zhu, Tingjun Hou
Deciphering the structural determinants of protein-protein interactions (PPIs) is essential to gain a deep understanding of many important biological functions in the living cells. Computational approaches for the structural modeling of PPIs, such as protein-protein docking, are quite needed to complement existing experimental techniques. The reliability of a protein-protein docking method is dependent on the ability of the scoring function to accurately distinguish the near-native binding structures from a huge number of decoys...
December 28, 2017: Journal of Cheminformatics
Nawsad Alam, Oriel Goldstein, Bing Xia, Kathryn A Porter, Dima Kozakov, Ora Schueler-Furman
Peptide-protein interactions contribute a significant fraction of the protein-protein interactome. Accurate modeling of these interactions is challenging due to the vast conformational space associated with interactions of highly flexible peptides with large receptor surfaces. To address this challenge we developed a fragment based high-resolution peptide-protein docking protocol. By streamlining the Rosetta fragment picker for accurate peptide fragment ensemble generation, the PIPER docking algorithm for exhaustive fragment-receptor rigid-body docking and Rosetta FlexPepDock for flexible full-atom refinement of PIPER docked models, we successfully addressed the challenge of accurate and efficient global peptide-protein docking at high-resolution with remarkable accuracy, as validated on a small but representative set of peptide-protein complex structures well resolved by X-ray crystallography...
December 27, 2017: PLoS Computational Biology
Walhan Alshaer, Nida Ababneh, Mamon Hatmal, Heba Izmirli, Moujab Choukeife, Alaa Shraim, Nour Sharar, Aya Abu-Shiekah, Fadwa Odeh, Abeer Al Bawab, Abdalla Awidi, Said Ismail
Aptamers are molecules that reveal highly complex and refined molecular recognition properties. These molecules are capable of binding with high affinity and selectivity to targets, ranging from small molecules to whole living cells. Several aptamers have been selected for targeting cellular proteins and they have also used in developing therapeutics and diagnostic strategies. Epithelial cell adhesion molecule (EpCAM) is considered as a cancer stem cell (CSC) biomarker and one of the most promising targets for aptamer selection against CSCs...
2017: PloS One
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