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"protein docking"

Roshanak Farhoodi, Bahar Akbal-Delibas, Nurit Haspel
Discriminating native-like structures from false positives with high accuracy is one of the biggest challenges in protein-protein docking. While there is an agreement on the existence of a relationship between various favorable intermolecular interactions (e.g., Van der Waals, electrostatic, and desolvation forces) and the similarity of a conformation to its native structure, the precise nature of this relationship is not known. Existing protein-protein docking methods typically formulate this relationship as a weighted sum of selected terms and calibrate their weights by using a training set to evaluate and rank candidate complexes...
October 17, 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
Thom Vreven, Brian G Pierce, Tyler M Borrman, Zhiping Weng
We report the performance of our protein-protein docking pipeline, including the ZDOCK rigid-body docking algorithm, on 19 targets in CAPRI rounds 28-34. Following the docking step, we reranked the ZDOCK predictions using the IRAD scoring function, pruned redundant predictions, performed energy landscape analysis, and utilized our interface prediction approach RCF. In addition, we applied constraints to the search space based on biological information that we culled from the literature, which increased the chance of making a correct prediction...
October 7, 2016: Proteins
Jinchao Yu, Jessica Andreani, Françoise Ochsenbein, Raphaël Guerois
Computational protein-protein docking is of great importance for understanding protein interactions at the structural level. CAPRI (Critical Assessment of PRediction of Interactions) experiments provide the protein docking community with a unique opportunity to blindly test methods based on real-life cases and help accelerate methodology development. For CAPRI rounds 28-35, we used an automatic docking pipeline integrating the coarse-grained co-evolution-based potential InterEvScore. This score was developed to exploit the information contained in the multiple sequence alignments of binding partners and selectively recognize co-evolved interfaces...
October 4, 2016: Proteins
Dudipeta Vasu, Pasupuleti Santhosh Kumar, Uppu Venkateswara Prasad, Vimjam Swarupa, Sthanikam Yeswanth, Lokanathan Srikanth, Manne Mudhu Sunitha, Abhijith Choudhary, Potukuchi Venkata Gurunadha Krishna Sarma
BACKGROUND: When Staphylococcus aureus is grown in the presence of high concentration of external glucose, this sugar is phosphorylated by glucokinase (glkA) to form glucose-6-phosphate. This product subsequently enters into anabolic phase, which favors biofilm formation. The presence of ROK (repressor protein, open reading frame, sugar kinase) motif, phosphate-1 and -2 sites, and tyrosine kinase sites in glkA of S. aureus indicates that phosphorylation must regulate the glkA activity...
October 1, 2016: Iranian Biomedical Journal
Thirupathi Dasari, Bhargavi Kondagari, Ramasree Dulapalli, Aboubakr Haredi Abdelmonsef, Thirupathi Mukkera, Lavanya Souda Padmarao, Vasavi Malkhed, Uma Vuruputuri
Cancer is a class of diseases characterized by uncontrolled cell growth. Every year More than 2 million people are affected by the disease. Rho family proteins are actively involved in cytoskeleton regulation. Over-expression of Rho family proteins show oncogenic activity and promote cancer progression. In the present work RhoG protein is considered as novel target of cancer. It is a member of Rho family and Rac subfamily protein, which plays pivotal role in regulation of microtubule formation, cell migration and contributes in cancer progression...
October 3, 2016: Journal of Biomolecular Structure & Dynamics
Jianqiong Yang, Haiqing Liu, Linfu Li, Hai Liu, Weimei Shi, Xiaoliang Yuan, Longhuo Wu
IRE1 signaling is the most evolutionarily conserved branch in the UPR. IRE1 is an ER stress sensor and provides a structure-based platform for the unfolded proteins docking, which causes the luminal domain conformational change and oligomerization. This self-association of IRE1 facilitates the phosphorylation of activation loop, which unlocks the auto-inhibition in the kinase domain. The activating mechanistic cascade is thus initiated to induce DFG-in conformational change and movement of αC-helix to the active site...
September 27, 2016: Current Medicinal Chemistry
Nicholas A Marze, Jeliazko R Jeliazkov, Shourya Sonkar Roy Burman, Scott E Boyken, Frank DiMaio, Jeffrey J Gray
The 28th-35th rounds of the Critical Assessment of PRotein Interactions (CAPRI) served as a practical benchmark for our RosettaDock protein-protein docking protocols, highlighting strengths and weaknesses of the approach. We achieved acceptable or better quality models in three out of 11 targets. For the two α-repeat protein-green fluorescent protein (αrep-GFP) complexes, we used a novel ellipsoidal partial-global docking method (Ellipsoidal Dock) to generate models with 2.2 Å/1.5 Å interface RMSD, capturing 49%/42% of the native contacts, for the 7-/5-repeat αrep complexes...
September 26, 2016: Proteins
Ying Wang, Ying Wāng, Yingnv Gao, Yan Li, Jia-Ning Wan, Rui-Heng Yang, Wen-Jun Mao, Chen-Li Zhou, Li-Hua Tang, Ming Gong, Ying-Ying Wu, Da-Peng Bao
Volvaria volvacea (Bull. ex Fr.) Sing, an important edible and medicinal macro-fungus, has been used to remedy various diseases for hundreds of years in East Asia. To identify key proteins with the unique therapeutic activity in V. volvacea, we conducted a genome-wide comparison of V. volvacea protein families and those of other edible fungi that lack therapeutic functions and identified 7 fungal immunomodulatory proteins (FIPs) in V. volvacea. Based on the predicted physiological and biochemical characteristics of the 7 FIPs, the novel Fip-vvo82 was inferred to have high immunomodulatory activity; this was confirmed by molecular and immunological experiments and further characterized by modeling the 3D structure and protein-protein docking...
September 20, 2016: Journal of Chemical Information and Modeling
Parisa Ghanavatian, Khosrow Khalifeh, Vahab Jafarian
Brazzein (Brz) is a member of sweet-tasting protein containing four disulfide bonds. It was reported as a compact and heat-resistant protein. Here, we have used site-directed mutagenesis and replaced a surface-exposed alanine with aspartic acid (A19D mutant), lysine (A19K mutant) and glycine (A19G mutant). Activity comparisons of wild-type (WT) and mutants using taste panel test procedure showed that A19G variant has the same activity as WT protein. However, introduction of a positive charge in A19K mutant led to significant increase in Brz's sweetness, while A19D has reduced sweetness compared to WT protein...
September 8, 2016: Biochimie
Martiniano Bello, Mixtli J Torres, Alfonso Méndez-Tenorio, José Correa-Basurto
Peripheral myelin protein 22 (PMP22) resides in the plasma membrane and is required for myelin formation in the peripheral nervous system. Excess PMP22 mutants accumulate in the endoplasmic reticulum (ER) resulting in the inherited neuropathies of Charcot-Marie-Tooth disease. However, there was no evidence of the structure of PMP22 or how mutations affect its folding. Therefore, in this study, we combined bioinformatics and homology modeling approaches to obtain three-dimensional native and mutated PMP22 models and its anchoring to a POPC membrane, submitted to ...
October 5, 2016: Journal of Biomolecular Structure & Dynamics
Taniya Saha, Deblina Guha, Argha Manna, Abir Kumar Panda, Jyotsna Bhat, Subhrangsu Chatterjee, Gaurisankar Sa
p53 preserves genomic integrity by restricting anomaly at the gene level. Till date, limited information is available for cytosol to nuclear shuttling of p53; except microtubule-based trafficking route, which utilizes minus-end directed motor dynein. The present study suggests that monomeric actin (G-actin) guides p53 traffic towards the nucleus. Histidine-tag pull-down assay using purified p53(1-393)-His and G-actin confirms direct physical association between p53 and monomeric G-actin. Co-immunoprecipitation data supports the same...
2016: Scientific Reports
Wesley J Mair, Weiwei Deng, Jonathan G L Mullins, Samuel West, Penghao Wang, Naghmeh Besharat, Simon R Ellwood, Richard P Oliver, Francisco J Lopez-Ruiz
Pyrenophora teres f. sp. teres is the cause of net form of net blotch (NFNB), an economically important foliar disease in barley (Hordeum vulgare). Net and spot forms of net blotch are widely controlled using site-specific systemic fungicides. Although resistance to succinate dehydrogenase inhibitors and quinone outside inhibitors has been addressed before in net blotches, mechanisms controlling demethylation inhibitor resistance have not yet been reported at the molecular level. Here we report the isolation of strains of NFNB in Australia since 2013 resistant to a range of demethylase inhibitor fungicides...
2016: Frontiers in Microbiology
Emilie Neveu, David W Ritchie, Petr Popov, Sergei Grudinin
MOTIVATION: Docking prediction algorithms aim to find the native conformation of a complex of proteins from knowledge of their unbound structures. They rely on a combination of sampling and scoring methods, adapted to different scales. Polynomial Expansion of Protein Structures and Interactions for Docking (PEPSI-Dock) improves the accuracy of the first stage of the docking pipeline, which will sharpen up the final predictions. Indeed, PEPSI-Dock benefits from the precision of a very detailed data-driven model of the binding free energy used with a global and exhaustive rigid-body search space...
September 1, 2016: Bioinformatics
Daisuke Kuroda, Jeffrey J Gray
Conformational changes of proteins that occur upon binding typically confound computational docking algorithms. In this study, we test computational methods to capture protein backbone conformational change related to binding. To address how well existing algorithms can sample bound-like backbones, we query seven techniques including Monte Carlo-based sampling, molecular dynamics, and normal mode analysis. All methods tested rarely sample near-bound states from the unbound conformation. Nevertheless, the direction of the predicted motions overlap with the actual conformational change...
October 4, 2016: Structure
Sankar Basu, Björn Wallner
The state-of-the-art to assess the structural quality of docking models is currently based on three related yet independent quality measures: Fnat, LRMS, and iRMS as proposed and standardized by CAPRI. These quality measures quantify different aspects of the quality of a particular docking model and need to be viewed together to reveal the true quality, e.g. a model with relatively poor LRMS (>10Å) might still qualify as 'acceptable' with a descent Fnat (>0.50) and iRMS (<3.0Å). This is also the reason why the so called CAPRI criteria for assessing the quality of docking models is defined by applying various ad-hoc cutoffs on these measures to classify a docking model into the four classes: Incorrect, Acceptable, Medium, or High quality...
2016: PloS One
Jinchao Yu, Raphaël Guerois
MOTIVATION: Protein-protein docking methods are of great importance for understanding interactomes at the structural level. It has become increasingly appealing to use not only experimental structures but also homology models of unbound subunits as input for docking simulations. So far we are missing a large scale assessment of the success of rigid-body free docking methods on homology models. RESULTS: We explored how we could benefit from comparative modeling of unbound subunits to expand docking benchmark datasets...
August 22, 2016: Bioinformatics
Lim Heo, Hasup Lee, Chaok Seok
Protein-protein docking methods have been widely used to gain an atomic-level understanding of protein interactions. However, docking methods that employ low-resolution energy functions are popular because of computational efficiency. Low-resolution docking tends to generate protein complex structures that are not fully optimized. GalaxyRefineComplex takes such low-resolution docking structures and refines them to improve model accuracy in terms of both interface contact and inter-protein orientation. This refinement method allows flexibility at the protein interface and in the overall docking structure to capture conformational changes that occur upon binding...
2016: Scientific Reports
Rui M Almeida, Simone Dell'Acqua, Ludwig Krippahl, José J G Moura, Sofia R Pauleta
The importance of understanding interactomes makes preeminent the study of protein interactions and protein complexes. Traditionally, protein interactions have been elucidated by experimental methods or, with lower impact, by simulation with protein docking algorithms. This article describes features and applications of the BiGGER docking algorithm, which stands at the interface of these two approaches. BiGGER is a user-friendly docking algorithm that was specifically designed to incorporate experimental data at different stages of the simulation, to either guide the search for correct structures or help evaluate the results, in order to combine the reliability of hard data with the convenience of simulations...
2016: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Nanjie Deng, Ashley Hoyte, Yara E Mansour, Mosaad S Mohamed, James R Fuchs, Alan N Engelman, Mamuka Kvaratskhelia, Ronald Levy
Allosteric HIV-1 integrase (IN) inhibitors (ALLINIs) bind at the dimer interface of the IN catalytic core domain (CCD), and potently inhibit HIV-1 by promoting aberrant, higher-order IN multimerization. Little is known about the structural organization of the inhibitor-induced IN multimers and important questions regarding how ALLINIs promote aberrant IN multimerization remain to be answered. On the basis of physical chemistry principles and from our analysis of experimental information, we propose that inhibitor-induced multimerization is mediated by ALLINIs directly promoting inter-subunit interactions between the CCD dimer and a C-terminal domain (CTD) of another IN dimer...
August 9, 2016: Protein Science: a Publication of the Protein Society
Junichi Iwakiri, Michiaki Hamada, Kiyoshi Asai, Tomoshi Kameda
RNA-protein interactions play fundamental roles in many biological processes. To understand these interactions, it is necessary to know the three-dimensional structures of RNA-protein complexes. However, determining the tertiary structure of these complexes is often difficult, suggesting that an accurate rigid body docking for RNA-protein complexes is needed. In general, the rigid body docking process is divided into two steps: generating candidate structures from the individual RNA and protein structures and then narrowing down the candidates...
September 13, 2016: Journal of Chemical Theory and Computation
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