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https://www.readbyqxmd.com/read/29343185/exploring-protein-protein-intermolecular-recognition-between-meprin-%C3%AE-and-endogenous-protease-regulator-cystatinc-coupled-with-pharmacophore-elucidation
#1
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
https://www.readbyqxmd.com/read/29329283/modeling-the-assembly-order-of-multimeric-heteroprotein-complexes
#2
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 12, 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29326158/reciprocal-spatiotemporally-controlled-apoptosis-regulates-wolffian-duct-cloaca-fusion
#3
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
https://www.readbyqxmd.com/read/29315602/comparison-of-two-docking-methods-for-peptide-protein-interactions
#4
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
https://www.readbyqxmd.com/read/29305211/isolation-purification-and-characterization-of-proteinaceous-fungal-%C3%AE-amylase-inhibitor-from-rhizome-of-cheilocostus-speciosus-j-koenig-c-d-specht
#5
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
https://www.readbyqxmd.com/read/29298877/molecular-basis-for-potentiation-of-cx36-gap-junction-channel-conductance-by-n-alcohols-and-general-anesthetics
#6
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
https://www.readbyqxmd.com/read/29290793/epigenomic-characterization-of-a-p53-regulated-3p22-2-tumor-suppressor-that-inhibits-stat3-phosphorylation-via-protein-docking-and-is-frequently-methylated-in-esophageal-and-other-carcinomas
#7
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
https://www.readbyqxmd.com/read/29282565/hawkrank-a-new-scoring-function-for-protein-protein-docking-based-on-weighted-energy-terms
#8
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
https://www.readbyqxmd.com/read/29281622/high-resolution-global-peptide-protein-docking-using-fragments-based-piper-flexpepdock
#9
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
https://www.readbyqxmd.com/read/29245156/selection-and-targeting-of-epcam-protein-by-ssdna-aptamer
#10
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
https://www.readbyqxmd.com/read/29241118/plhint-a-knowledge-driven-computational-approach-based-on-the-intermolecular-h-bond-interactions-at-the-protein-ligand-interface-from-docking-solutions
#11
Sivakumar Prasanth Kumar
The tendency of docking scoring functions to generate crystal close conformations of ligands bound to protein structures face limitations in not reproducing the exact crystal intermolecular contacts in dock poses. Intermolecular H bond contacts enumerated at the protein-docked ligand interface can be used to train scoring models and improve virtual screening performance. There is a need to incorporate additional knowledge of protein-ligand H bond contacts in extension to crystal contacts from docking solutions within the reproducibility efficiency of the docking program...
December 6, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/29226078/identification-and-in%C3%A2-silico-structural-analysis-of-gallus-gallus-protein-arginine-methyltransferase-4-prmt4
#12
Hannah Berberich, Felix Terwesten, Sinja Rakow, Peeyush Sahu, Caroline Bouchard, Marion Meixner, Sjaak Philipsen, Peter Kolb, Uta-Maria Bauer
Protein arginine methyltransferase 4 (PRMT4) is an essential epigenetic regulator of fundamental and conserved processes during vertebrate development, such as pluripotency and differentiation. Surprisingly, PRMT4 homologs have been identified in nearly all vertebrate classes except the avian genome. This raises the possibility that in birds PRMT4 functions are taken over by other PRMT family members. Here, we reveal the existence of a bona fide PRMT4 homolog in the chicken, Gallus gallus. Using a biochemical approach, we initially purified a putative chicken PRMT4 protein and thus provided the first evidence for the presence of an endogenous PRMT4-specific enzymatic activity toward histone H3 arginine 17 (H3R17) in avian cells...
December 2017: FEBS Open Bio
https://www.readbyqxmd.com/read/29218430/cpdock-the-complementarity-plot-for-docking-of-proteins-implementing-multi-dielectric-continuum-electrostatics
#13
Sankar Basu
The complementarity plot (CP) is an established validation tool for protein structures, applicable to both globular proteins (folding) as well as protein-protein complexes (binding). It computes the shape and electrostatic complementarities (Sm, Em) for amino acid side-chains buried within the protein interior or interface and plots them in a two-dimensional plot having knowledge-based probabilistic quality estimates for the residues as well as for the whole structure. The current report essentially presents an upgraded version of the plot with the implementation of the advanced multi-dielectric functionality (as in Delphi version 6...
December 7, 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/29212707/inherent-steroid-17%C3%AE-20-lyase-activity-in-defunct-cytochrome-p450-17a-enzymes
#14
Eric Gonzalez, Kevin M Johnson, Pradeep S Pallan, Thanh T N Phan, Wei Zhang, L I Lei, Zdzislaw Wawrzak, Francis K Yoshimoto, Martin Egli, F Peter Guengerich
Cytochrome P450 (P450) 17A1 catalyzes the oxidations of progesterone and pregnenolone and is the major source of androgens. The enzyme catalyzes both 17α-hydroxylation and a subsequent 17α, 20-lyase reaction, and several mechanisms have been proposed for the latter step. Zebrafish P450 17A2 catalyzes only the 17α-hydroxylations. We previously reported high similarity of the crystal structures of zebrafish P450 17A1 and 17A2 and human P450 17A1 (Pallan et al. (2015) J. Biol. Chem. 290, 3248- 3268). Five residues near the heme, which differed, were changed...
December 6, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29210581/modelling-of-human-fatty-acid-synthase-and-in-silico-docking-of-acyl-carrier-protein-domain-and-its-partner-catalytic-domains
#15
Rui P P Neves, Maria João Ramos, Pedro A Fernandes, Matilde Viegas
Human Fatty Acid Synthase (hFAS) is a megasynthase whose main function is de novo biosynthesis of saturated fatty acids. Interest has been drawn to this enzyme beyond its physiological role due to the association between high levels of hFAS and clinical conditions such as obesity, diabetes and cancer. Thus, it has become an undeniably attractive pharmacological target. Until now, no crystal structure of the complete hFAS is available, hindering attempts to fully understand this protein. Using homology modelling, we built a model of the entire megasynthase, encompassing all of its domains, including the Acyl Carrier Protein (ACP) and Thioesterase (TE) mobile domains absent in the crystal structure of mammalian Fatty Acid Synthase (FAS)...
December 6, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29185359/gualou-guizhi-decoction-reverses-brain-damage-with-cerebral-ischemic-stroke-multi-component-directed-multi-target-to-screen-calcium-overload-inhibitors-using-combination-of-molecular-docking-and-protein-protein-docking
#16
Juan Hu, Wen-Sheng Pang, Jing Han, Kuan Zhang, Ji-Zhou Zhang, Li-Dian Chen
Stroke is a disease of the leading causes of mortality and disability across the world, but the benefits of drugs curative effects look less compelling, intracellular calcium overload is considered to be a key pathologic factor for ischemic stroke. Gualou Guizhi decoction (GLGZD), a classical Chinese medicine compound prescription, it has been used to human clinical therapy of sequela of cerebral ischemia stroke for 10 years. This work investigated the GLGZD improved prescription against intracellular calcium overload could decreased the concentration of [Ca2+]i in cortex and striatum neurone of MCAO rats...
December 2018: Journal of Enzyme Inhibition and Medicinal Chemistry
https://www.readbyqxmd.com/read/29135287/molecular-modelling-studies-in-explaining-the-higher-gpvi-antagonistic-activity-of-the-racemic-2-4-methoxyphenylsulfonyl-2-3-4-9-tetrahydro-1h-pyrido-3-4-b-indole-3-carboxamide-than-its-enantiomers
#17
S S Bhunia, A K Saxena
The GPVI receptor on the platelets plays a major role in inhibiting arterial thrombosis with limited risk of bleeding and is considered a potential anti-thrombotic target for arterial thrombosis. In the reported anti-thrombotics, tetrahydropyridoindoles, the title compound was the best inhibitor of the collagen mediated platelet aggregation by antagonizing the platelet receptor GPVI. Interestingly, the racemic title compound showed better antagonism (IC50 racemate = 6.7 μM) than either of its enantiomers (IC50 S enantiomer = 25...
November 14, 2017: SAR and QSAR in Environmental Research
https://www.readbyqxmd.com/read/29099834/identification-of-small-molecules-uncoupling-the-notch-jagged-interaction-through-an-integrated-high-throughput-screening
#18
Natalia Platonova, Chiara Parravicini, Cristina Sensi, Alessandro Paoli, Michela Colombo, Antonino Neri, Ivano Eberini, Raffaella Chiaramonte
Notch signaling plays an important role in several cellular functions including growth, differentiation, cell fate determination and stemness. Increased Notch activity has been linked to several types of cancers. Activation of Notch signaling is triggered by the interaction of Notch receptors (Notch1-4) with 5 different ligands (Jagged1-2 and Dll1-3-4) expressed on the neighbouring cells. Currently, indirect approaches to inhibit Notch signalling are based on the inhibition of the key step of Notch activation catalyzed by the γ-Secretase and thereby affect several different γ-Secretase substrates; conversely direct strategies get advantage of antibody-based drugs...
2017: PloS One
https://www.readbyqxmd.com/read/29081606/molecular-dynamics-simulation-analysis-of-focal-adhesive-kinase-fak-docked-with-solanesol-as-an-anti-cancer-agent
#19
Betty Daneial, Jacob Paul Vazhappilly Joseph, Guruprasad Ramakrishna
Focal adhesion kinase (FAK) plays a primary role in regulating the activity of many signaling molecules. Increased FAK expression has been associated in a series of cellular processes like cell migration and survival. FAK inhibition by an anti cancer agent is critical. Therefore, it is of interest to identify, modify, design, improve and develop molecules to inhibit FAK. Solanesol is known to have inhibitory activity towards FAK. However, the molecular principles of its binding with FAK is unknown. Solanesol is a highly flexible ligand (25 rotatable bonds)...
2017: Bioinformation
https://www.readbyqxmd.com/read/29028891/on-the-mechanisms-of-protein-interactions-predicting-their-affinity-from-unbound-tertiary-structures
#20
Manuel Alejandro Marín-López, Joan Planas-Iglesias, Joaquim Aguirre-Plans, Jaume Bonet, Javier Garcia-Garcia, Narcis Fernandez-Fuentes, Baldo Oliva
Motivation: The characterization of the protein-protein association mechanisms is crucial to understanding how biological processes occur. It has been previously shown that the early formation of non-specific encounters enhances the realization of the stereospecific (i.e. native) complex by reducing the dimensionality of the search process. The association rate for the formation of such complex plays a crucial role in the cell biology and depends on how the partners diffuse to be close to each other...
September 27, 2017: Bioinformatics
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