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Protein interface prediction

Virginia P Ronchi, Elizabeth D Kim, Christopher M Summa, Jennifer M Klein, Arthur L Haas
To understand the mechanism for assembly of Lys(48)-linked polyubiquitin degradation signals, we previously demonstrated the E6AP/UBE3A ligase harbors two functionally-distinct E2~ubiquitin binding sites: a high-affinity Site 1 required for E6AP Cys(820)~ubiquitin thioester formation and a canonical Site 2 responsible for subsequent chain elongation. Ordered binding to Sites 1 and 2 is here revealed by observation of UbcH7~ubiquitin-dependent substrate inhibition of chain formation at micromolar concentrations...
September 18, 2017: Journal of Biological Chemistry
M Salvatore, N Shu, A Elofsson
SubCons is a recently developed method that predicts the subcellular localisation of a protein. It combines predictions from four predictors using a Random Forest classifier. Here, we present the user-friendly web-interface implementation of SubCons. Starting from a protein sequence, the server rapidly predicts the subcellular localisations of an individual protein. Additionally, the server accepts the submission of sets of proteins either by uploading the files or programmatically by using command line WSDL API scripts...
September 13, 2017: Protein Science: a Publication of the Protein Society
Robert Kammerer, Martin Mansfeld, Jana Hänske, Sophie Mißbach, Xiaocui He, Bernd Köllner, Susan Mouchantat, Wolfgang Zimmermann
BACKGROUND: Expansions of gene families are predictive for ongoing genetic adaptation to environmental cues. We describe such an expansion of the carcinoembryonic antigen (CEA) gene family in certain bat families. Members of the CEA family in humans and mice are exploited as cellular receptors by a number of pathogens, possibly due to their function in immunity and reproduction. The CEA family is composed of CEA-related cell adhesion molecules (CEACAMs) and secreted pregnancy-specific glycoproteins (PSGs)...
September 11, 2017: BMC Genomics
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
Farhad Ramezanghorbani, Cahit Dalgicdir, Mehmet Sayar
Many proteins display a marginally stable tertiary structure, which can be altered via external stimuli. Since a majority of coarse grained (CG) models are aimed at structure prediction, their success for an intrinsically disordered peptide's conformational space with marginal stability and sensitivity to external stimuli cannot be taken for granted. In this study, by using the LKα14 peptide as a test system, we demonstrate a bottom-up approach for constructing a multi-state CG model, which can capture the conformational behavior of this peptide in three distinct environments with a unique set of interaction parameters...
September 7, 2017: Journal of Chemical Physics
Yuji Tokunaga, Koh Takeuchi, Ichio Shimada
The dynamic property of a ligand in the receptor-bound state is an important metric to characterize the interactions in the ligand-receptor interface, and the development of an experimental strategy to quantify the amplitude of motions in the bound state is of importance to introduce the dynamic aspect into structure-guided drug development (SGDD). Fluorine modifications are frequently introduced at the hit-to-lead optimization stage to enhance the binding potency and other characteristics of a ligand. However, the effects of fluorine modifications are generally difficult to predict, owing to the pleiotropic nature of the interactions...
September 7, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Lei Pan, Christopher L Gardner, Fernando A Pagliai, Claudio F Gonzalez, Graciela L Lorca
In Liberibacter asiaticus, PrbP is an important transcriptional accessory protein that was found to regulate gene expression through interactions with the RNA polymerase β-subunit and a specific sequence on the promoter region. It was found that inactivation of PrbP, using the inhibitor tolfenamic acid, resulted in a significant decrease in the overall transcriptional activity of L. asiaticus, and the suppression of L. asiaticus infection in HLB symptomatic citrus seedlings. The molecular interactions between PrbP and tolfenamic acid, however, were yet to be elucidated...
2017: Frontiers in Microbiology
Kazunori D Yamada, Naoki Kunishima, Yoshinori Matsuura, Koshiro Nakai, Hisashi Naitow, Yoshinori Fukasawa, Kentaro Tomii
An alternative rational approach to improve protein crystals by using single-site mutation of surface residues is proposed based on the results of a statistical analysis using a compiled data set of 918 independent crystal structures, thereby reflecting not only the entropic effect but also other effects upon protein crystallization. This analysis reveals a clear difference in the crystal-packing propensity of amino acids depending on the secondary-structural class. To verify this result, a systematic crystallization experiment was performed with the biotin carboxyl carrier protein from Pyrococcus horikoshii OT3 (PhBCCP)...
September 1, 2017: Acta Crystallographica. Section D, Structural Biology
Martino Bertoni, Florian Kiefer, Marco Biasini, Lorenza Bordoli, Torsten Schwede
Cellular processes often depend on interactions between proteins and the formation of macromolecular complexes. The impairment of such interactions can lead to deregulation of pathways resulting in disease states, and it is hence crucial to gain insights into the nature of macromolecular assemblies. Detailed structural knowledge about complexes and protein-protein interactions is growing, but experimentally determined three-dimensional multimeric assemblies are outnumbered by complexes supported by non-structural experimental evidence...
September 5, 2017: Scientific Reports
Ria Biswas, Angshuman Bagchi
Protein-protein interactions (PPIs) are important in most of the biochemical processes. Hotspot amino acid residues in proteins are the most important contributors for proper protein-protein interactions. Hotspot amino acid residues have been looked down upon as important therapeutic targets in inhibiting PPIs. Interaction between TRAF6 and Ubc13 is a crucial point in the NFkB inflammatory pathway. Dysfunction of the NFkB pathway is associated with numerous human diseases including cancer and neurodenegeration disorders...
September 1, 2017: Computational Biology and Chemistry
Zhijun Qiu, Bo Zhou, Jiangfeng Yuan
Protein-protein interaction site (PPIS) prediction must deal with the diversity of interaction sites that limits their prediction accuracy. Use of proteins with unknown or unidentified interactions can also lead to missing interfaces. Such data errors are often brought into the training dataset. In response to these two problems, we used the minimum covariance determinant (MCD) method to refine the training data to build a predictor with better performance, utilizing its ability of removing outliers. In order to predict test data in practice, a method based on Mahalanobis distance was devised to select proper test data as input for the predictor...
September 1, 2017: Journal of Theoretical Biology
Priyanka Jain, R S Pawar, R S Pandey, Jitender Madan, Sulakshna Pawar, P K Lakshmi, M S Sudheesh
One of the unmet challenges in nanotechnology is to understand and establish the relationship between physicochemical properties of nanoparticles (NPs) and its biological interactions (bio-nano interactions). However, we are still far from assessing the biofate of NPs in a clear and unquestionable manner. Recent developments in the area of bio-nano interface and the understanding of protein corona (PC) has brought new insight in predicting biological interactions of NPs. PC refers to the spontaneous formation of an adsorbed layer of biomolecules on the surface of NPs in a biological environment...
August 26, 2017: Biotechnology Advances
Danielle Silva Araújo, Patrícia de Sousa Lima, Lilian Cristiane Baeza, Ana Flávia Alves Parente, Alexandre Melo Bailão, Clayton Luiz Borges, Célia Maria de Almeida Soares
Paracoccidioidomycosis is an important systemic mycosis caused by thermodimorphic fungi of the Paracoccidioides genus. During the infective process, the cell wall acts at the interface between the fungus and the host. In this way, the cell wall has a key role in growth, environment sensing and interaction, as well as morphogenesis of the fungus. Since the cell wall is absent in mammals, it may present molecules that are described as target sites for new antifungal drugs. Despite its importance, up to now few studies have been conducted employing proteomics in for the identification of cell wall proteins in Paracoccidioides spp...
August 24, 2017: Biochimica et Biophysica Acta
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
Scott A Hollingsworth, Brian D Nguyen, Georges Chreifi, Anton P Arce, Thomas L Poulos
Leishmania major peroxidase (LmP) is structurally and functionally similar to the well-studied yeast cytochrome c peroxidase (CCP). A recent Brownian dynamics study showed that L. major cytochrome c (LmCytc) associates with LmP by forming an initial complex with the N-terminal helix A of LmP, followed by a movement toward the electron transfer (ET) site observed in the LmP-LmCytc crystal structure. Critical to forming the active electron transfer complex is an intermolecular Arg-Asp ion pair at the center of the interface...
August 25, 2017: Journal of Chemical Information and Modeling
Anirban Purohit, Jennifer K England, Lauren G Douma, Farzaneh Tondnevis, Linda B Bloom, Marcia Levitus
Sliding clamps are ring-shaped oligomeric proteins that encircle DNA and associate with DNA polymerases for processive DNA replication. The dimeric Escherichia coli β-clamp is closed in solution but must adopt an open conformation to be assembled onto DNA by a clamp loader. To determine what factors contribute to the stability of the dimer interfaces in the closed conformation and how clamp dynamics contribute to formation of the open conformation, we identified conditions that destabilized the dimer and measured the effects of these conditions on clamp dynamics...
August 22, 2017: Biophysical Journal
Svetlana Tarnovskaya, Artem Kiselev, Anna Kostareva, Dmitrij Frishman
Idiopathic restrictive cardiomyopathy (RCM, MIM# 115210) is the least common type of cardiomyopathies, often of genetic origin. Recently we described a spectrum of variants-classified as pathogenic, likely pathogenic and variants of unknown significance-in 24 patients suffering from idiopathic RCM. Pathogenic variants, detected in half of the RCM cases, were found in sarcomeric and cytoskeletal genes that have a predominant role in the development of RCM. Here we have analyzed the structural consequences of these missense variants and predicted their effect on the function of three large groups of domains: intrinsically disordered regions (IDRs), fibronectin-type III (FnIII) domains, and immunoglobulin-like (Ig) domains...
August 22, 2017: Amino Acids
Chijioke N Umunnakwe, Karin S Dorman, Drena Dobbs, Susan Carpenter
BACKGROUND: Rev-like proteins are post-transcriptional regulatory proteins found in several retrovirus genera, including lentiviruses, betaretroviruses, and deltaretroviruses. These essential proteins mediate the nuclear export of incompletely spliced viral RNA, and act by tethering viral pre-mRNA to the host CRM1 nuclear export machinery. Although all Rev-like proteins are functionally homologous, they share less than 30% sequence identity. In the present study, we computationally assessed the extent of structural homology among retroviral Rev-like proteins within a phylogenetic framework...
August 22, 2017: Retrovirology
Mateusz Kurcinski, Maciej Blaszczyk, Maciej Pawel Ciemny, Andrzej Kolinski, Sebastian Kmiecik
BACKGROUND: The characterization of protein-peptide interactions is a challenge for computational molecular docking. Protein-peptide docking tools face at least two major difficulties: (1) efficient sampling of large-scale conformational changes induced by binding and (2) selection of the best models from a large set of predicted structures. In this paper, we merge an efficient sampling technique with external information about side-chain contacts to sample and select the best possible models...
August 18, 2017: Biomedical Engineering Online
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
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