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Protein interface prediction

Raffaele Raucci, Elodie Laine, Alessandra Carbone
Several models estimating the strength of the interaction between proteins in a complex have been proposed. By exploring the geometry of contact distribution at protein-protein interfaces, we provide an improved model of binding energy. Local interaction signal analysis (LISA) is a radial function based on terms describing favorable and non-favorable contacts obtained by density functional theory, the support-core-rim interface residue distribution, non-interacting charged residues and secondary structures contribution...
April 28, 2018: Structure
Aleksander Kuriata, Aleksandra Maria Gierut, Tymoteusz Oleniecki, Maciej Pawel Ciemny, Andrzej Kolinski, Mateusz Kurcinski, Sebastian Kmiecik
Classical simulations of protein flexibility remain computationally expensive, especially for large proteins. A few years ago, we developed a fast method for predicting protein structure fluctuations that uses a single protein model as the input. The method has been made available as the CABS-flex web server and applied in numerous studies of protein structure-function relationships. Here, we present a major update of the CABS-flex web server to version 2.0. The new features include: extension of the method to significantly larger and multimeric proteins, customizable distance restraints and simulation parameters, contact maps and a new, enhanced web server interface...
May 14, 2018: Nucleic Acids Research
M Saifur Rahman, Swakkhar Shatabda, Sanjay Saha, M Kaykobad, M Sohel Rahman
A DNA-binding protein (DNA-BP) is a protein that can bind and interact with a DNA. Identification of DNA-BPs using experimental methods is expensive as well as time consuming. As such, fast and accurate computational methods are sought for predicting whether a protein can bind with a DNA or not. In this paper, we focus on building a new computational model to identify DNA-BPs in an efficient and accurate way. Our model extracts meaningful information directly from the protein sequences, without any dependence on functional domain or structural information...
May 10, 2018: Journal of Theoretical Biology
M Brighenti, S Govindasamy-Lucey, J J Jaeggi, M E Johnson, J A Lucey
Manufacture of cream cheese involves the formation of an initial acid-induced gel made from high-fat milk, followed by a series of processing steps including shearing, heating, and dewatering that complete the conversion of the acid gel into a complex cheese product. We investigated 2 critical parameters for their effect on the initial gel: homogenization pressure (HP) of the high-fat cheese milk, and fermentation temperature (FT). The impact of a low (10 MPa) and high (25 MPa) HP, and low (20°C) and high (26°C) FT were investigated for their effects on rheological and textural properties of acid-induced gels...
May 9, 2018: Journal of Dairy Science
Megha Abbey, Matthias Gaestel, Manoj B Menon
Septins are conserved cytoskeletal proteins with unique filament forming capabilities and roles in cytokinesis and cell morphogenesis. Septins undergo hetero-oligomerization and assemble into higher order structures including filaments, rings and cages. Hetero- and homotypic interactions of septin isoforms involve alternating GTPase (G)-domain interfaces and those mediated by N- and C-terminal extensions. While most septins bind GTP, display weak GTP-hydrolysis activity and incorporate guanine nucleotides in their interaction interfaces, studies using GTPase-inactivating mutations have failed to conclusively establish a crucial role for GTPase activity in mediating septin functions...
May 10, 2018: Cytoskeleton
Layla Hirsh, Lisanna Paladin, Damiano Piovesan, Silvio C E Tosatto
RepeatsDB-lite ( is a web server for the prediction of repetitive structural elements and units in tandem repeat (TR) proteins. TRs are a widespread but poorly annotated class of non-globular proteins carrying heterogeneous functions. RepeatsDB-lite extends the prediction to all TR types and strongly improves the performance both in terms of computational time and accuracy over previous methods, with precision above 95% for solenoid structures. The algorithm exploits an improved TR unit library derived from the RepeatsDB database to perform an iterative structural search and assignment...
May 9, 2018: Nucleic Acids Research
Chloé Quignot, Julien Rey, Jinchao Yu, Pierre Tufféry, Raphaël Guerois, Jessica Andreani
Computational protein docking is a powerful strategy to predict structures of protein-protein interactions and provides crucial insights for the functional characterization of macromolecular cross-talks. We previously developed InterEvDock, a server for ab initio protein docking based on rigid-body sampling followed by consensus scoring using physics-based and statistical potentials, including the InterEvScore function specifically developed to incorporate co-evolutionary information in docking. InterEvDock2 is a major evolution of InterEvDock which allows users to submit input sequences - not only structures - and multimeric inputs and to specify constraints for the pairwise docking process based on previous knowledge about the interaction...
May 8, 2018: Nucleic Acids Research
Carolina Carrillo-Carrión, Marta Gallego, Wolfgang J Parak, Mónica Carril
Understanding the interaction of nanoparticles with proteins and how this interaction modifies the nanoparticles’ surface is crucial before their use for biomedical applications. Since fluorinated materials are emerging as potential imaging probes and delivery vehicles, their interaction with proteins of biological interest must be studied in order to be able to predict their performance in real scenarios. It is known that fluorinated planar surfaces may repel the unspecific adsorption of proteins but little is known regarding the same process on fluorinated nanoparticles due to the scarce examples in the literature...
May 8, 2018: Materials
Pauline Bardin, Emmeline Marchal-Duval, Florence Sonneville, Sabine Blouquit-Laye, Nathalie Rousselet, Philippe Le Rouzic, Harriet Corvol, Olivier Tabary
Cystic fibrosis (CF) is the most common lethal genetic disease, caused by CFTR (cystic fibrosis transmembrane conductance regulator) gene mutations. CF is characterized by an ionic imbalance and thickened mucus, which impair mucociliary clearance, promote bacterial colonization, and the establishment of infection/inflammation cycles. However, the origin of this inflammation remains unclear, although microRNA (miRNA) are suspected to be involved. MiRNA are small non-coding RNA that bind to the 3'-untranslated regions (UTR) of target gene mRNA, thereby repressing their translation and/or inducing their degradation...
May 7, 2018: Journal of Pathology
Darwin Yu Fu, Jens Meiler
RosettaLigand is a protein-small-molecule (ligand) docking software capable of predicting binding poses and is used for virtual screening of medium-sized ligand libraries. Structurally similar small molecules are generally found to bind in the same pose to one binding pocket, despite some prominent exceptions. To make use of this information, we have developed RosettaLigandEnsemble (RLE). RLE docks a superimposed ensemble of congeneric ligands simultaneously. The program determines a well-scoring overall pose for this superimposed ensemble before independently optimizing individual protein-small-molecule interfaces...
April 30, 2018: ACS Omega
Manju Narwal, Harvijay Singh, Shivendra Pratap, Anjali Malik, Richard J Kuhn, Pravindra Kumar, Shailly Tomar
Chikungunya virus (CHIKV), a mosquito-borne pathogenic alphavirus is a growing public health threat. No vaccines or antiviral drug is currently available in the market for chikungunya treatment. nsP2pro, the viral cysteine protease, carries out an essential function of nonstructural polyprotein processing and forms four nonstructural proteins (nsPs) that makes the replication complex, hence constitute a promising drug target. In this study, crystal structure of nsP2pro has been determined at 2.59 Ǻ, which reveals that the protein consists of two subdomains: N-terminal protease subdomain and C-terminal methyltransferase subdomain...
May 3, 2018: International Journal of Biological Macromolecules
Frederick Johannes Clasen, Rian Ewald Pierneef, Bernard Slippers, Oleg Reva
BACKGROUND: Genomic islands (GIs) are inserts of foreign DNA that have potentially arisen through horizontal gene transfer (HGT). There are evidences that GIs can contribute significantly to the evolution of prokaryotes. The acquisition of GIs through HGT in eukaryotes has, however, been largely unexplored. In this study, the previously developed GI prediction tool, SeqWord Gene Island Sniffer (SWGIS), is modified to predict GIs in eukaryotic chromosomes. Artificial simulations are used to estimate ratios of predicting false positive and false negative GIs by inserting GIs into different test chromosomes and performing the SWGIS v2...
May 3, 2018: BMC Genomics
Ellen Koepf, Rudolf Schroeder, Gerald Brezesinski, Wolfgang Friess
The tendency of protein pharmaceuticals to form aggregates is a major challenge during formulation development, as aggregation affects quality and safety of the product. In particular, the formation of large native-like particles in the context of liquid-air interfacial stress is a well-known but not fully understood problem. Focusing on the two most fundamental criteria of protein formulation affecting protein-protein interaction, the impact of pH and ionic strength on the interaction parameter A∗ 2 and its link to aggregation upon mechanical stress was investigated...
April 30, 2018: European Journal of Pharmaceutics and Biopharmaceutics
Zheqiong Tan, Lanbo Xiao, Min Tang, Fang Bai, Jiangjiang Li, Liling Li, Feng Shi, Namei Li, Yueshuo Li, Qianqian Du, Jingchen Lu, Xinxian Weng, Wei Yi, Hanwen Zhang, Jia Fan, Jian Zhou, Qiang Gao, José N Onuchic, Ann M Bode, Xiangjian Luo, Ya Cao
Nasopharyngeal carcinoma (NPC) has a particularly high prevalence in southern China, southeastern Asia and northern Africa. Radiation resistance remains a serious obstacle to successful treatment in NPC. This study aimed to explore the metabolic feature of radiation-resistant NPC cells and identify new molecular-targeted agents to improve the therapeutic effects of radiotherapy in NPC. Methods : Radiation-responsive and radiation-resistant NPC cells were used as the model system in vitro and in vivo . Metabolomics approach was used to illustrate the global metabolic changes...
2018: Theranostics
Aleksandra I Jarmolinska, Michal Kadlof, Pawel Dabrowski-Tumanski, Joanna I Sulkowska
Motivation: Over 25% of protein structures possess unresolved fragments. On the other hand, approximately 6% of protein chains have non-trivial topology (and form knots, slipknots, lassos, and links). As the topology is fundamental for the proper function of proteins, modeling of topologically correct structures is decisive in various fields, including biophysics, biotechnology, and molecular biology. However, none of the currently existing tools take into account the topology of the model and those which could be modified to include topology, demand experience in bioinformatics, protein topology and knot theory...
April 30, 2018: Bioinformatics
Clement Mercier, Sophie Hodin, Zhiguo He, Nathalie Perek, Xavier Delavenne
The RPMI 2650 cell line has been described as a potent model of the human nasal mucosa. Nevertheless, pharmacological data are still insufficient and the role of drug efflux transporters has not been fully elucidated. We therefore pursued the pharmacological characterization of this model, initially investigating the expression of four well-known adenosine triphosphate [ATP]-binding cassette (ABC) transporters (P-glycoprotein (P-gp), multidrug resistance associated protein (MRP)1, MRP2 and breast cancer resistance protein (BCRP)) by means of ELISA and immunofluorescence staining...
April 30, 2018: Molecular Pharmaceutics
Spencer Bliven, Aleix Lafita, Althea Parker, Guido Capitani, Jose M Duarte
A correct assessment of the quaternary structure of proteins is a fundamental prerequisite to understanding their function, physico-chemical properties and mode of interaction with other proteins. Currently about 90% of structures in the Protein Data Bank are crystal structures, in which the correct quaternary structure is embedded in the crystal lattice among a number of crystal contacts. Computational methods are required to 1) classify all protein-protein contacts in crystal lattices as biologically relevant or crystal contacts and 2) provide an assessment of how the biologically relevant interfaces combine into a biological assembly...
April 30, 2018: PLoS Computational Biology
Semanti Ghosh, Angshuman Bagchi
Sulfur metabolism is one of the oldest known biochemical processes. Chemotrophic or phototrophic proteobacteria, through the dissimilatory pathway, use sulfate, sulfide, sulfite, thiosulfate or elementary sulfur by either reductive or oxidative mechanisms. During anoxygenic photosynthesis, anaerobic sulfur oxidizer Allochromatium vinosum forms sulfur globules that are further oxidized by dsr operon. One of the key redox enzymes in reductive or oxidative sulfur metabolic pathways is the DsrAB protein complex...
April 26, 2018: Journal of Molecular Modeling
Joshi Stephen, Sheela Nampoothiri, Aditi Banerjee, Nathanial J Tolman, Josef Martin Penninger, Ullrich Elling, Chukwuma A Agu, John D Burke, Kalpana Devadathan, Rajesh Kannan, Yan Huang, Peter J Steinbach, Susan A Martinis, William A Gahl, May Christine V Malicdan
Progressive microcephaly and neurodegeneration are genetically heterogenous conditions, largely associated with genes that are essential for the survival of neurons. In this study, we interrogate the genetic etiology of two siblings from a non-consanguineous family with severe early onset of neurological manifestations. Whole exome sequencing identified novel compound heterozygous mutations in VARS that segregated with the proband: a missense (c.3192G>A; p.Met1064Ile) and a splice site mutation (c.1577-2A>G)...
April 24, 2018: Human Genetics
Merve Dogangun, Paul E Ohno, Dongyue Liang, Alicia C McGeachy, Ariana Gray Bé, Naomi Dalchand, Tianzhe Li, Qiang Cui, Franz M Geiger
We report vibrational sum frequency generation (SFG) spectra in which the C-H stretches of lipid alkyl tails in fully hydrogenated single- and dual-component supported lipid bilayers are detected along with the O-H stretching continuum above the bilayer. As the salt concentration is increased from ~10 µM to 0.1 M, the SFG intensities in the O-H stretching region decrease by a factor of 2, consistent with significant absorptive-dispersive mixing between χ(2) and χ(3) contributions to the SFG signal generation process from charged interfaces...
April 24, 2018: Journal of Physical Chemistry. B
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