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Lukasz kurgan

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https://www.readbyqxmd.com/read/27801519/computational-prediction-of-protein-secondary-structure-from-sequence
#1
Fanchi Meng, Lukasz Kurgan
Secondary structure of proteins refers to local and repetitive conformations, such as α-helices and β-strands, which occur in protein structures. Computational prediction of secondary structure from protein sequences has a long history with three generations of predictive methods. This unit summarizes several recent third-generation predictors. We discuss their inputs and outputs, availability, and predictive performance and explain how to perform and interpret their predictions. We cover methods for the prediction of the 3-class secondary structure states (helix, strand, and coil) as well as the 8-class secondary structure states...
November 1, 2016: Current Protocols in Protein Science
https://www.readbyqxmd.com/read/27787828/prediction-of-disordered-rna-dna-and-protein-binding-regions-using-disordpbind
#2
Zhenling Peng, Chen Wang, Vladimir N Uversky, Lukasz Kurgan
Intrinsically disordered proteins and regions (IDPs and IDRs) are involved in a wide range of cellular functions and they often facilitate interactions with RNAs, DNAs, and proteins. Although many computational methods can predict IDPs and IDRs in protein sequences, only a few methods predict their functions and these functions primarily concern protein binding. We describe how to use the first computational method DisoRDPbind for high-throughput prediction of multiple functions of disordered regions. Our method predicts the RNA-, DNA-, and protein-binding residues located in IDRs in the input protein sequences...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27663889/what-are-the-structural-features-that-drive-partitioning-of-proteins-in-aqueous-two-phase-systems
#3
Zhonghua Wu, Gang Hu, Kui Wang, Boris Yu Zaslavsky, Lukasz Kurgan, Vladimir N Uversky
Protein partitioning in aqueous two-phase systems (ATPSs) represents a convenient, inexpensive, and easy to scale-up protein separation technique. Since partition behavior of a protein dramatically depends on an ATPS composition, it would be highly beneficial to have reliable means for (even qualitative) prediction of partitioning of a target protein under different conditions. Our aim was to understand which structural features of proteins contribute to partitioning of a query protein in a given ATPS. We undertook a systematic empirical analysis of relations between 57 numerical structural descriptors derived from the corresponding amino acid sequences and crystal structures of 10 well-characterized proteins and the partition behavior of these proteins in 29 different ATPSs...
September 24, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27377881/autophagy-related-intrinsically-disordered-proteins-in-intra-nuclear-compartments
#4
Insung Na, Fanchi Meng, Lukasz Kurgan, Vladimir N Uversky
Recent analyses indicated that autophagy can be regulated via some nuclear transcriptional networks and many important players in the autophagy and other forms of programmed cell death are known to be intrinsically disordered. To this end, we analyzed similarities and differences in the intrinsic disorder distribution of nuclear and non-nuclear proteins related to autophagy. We also looked at the peculiarities of the distribution of the intrinsically disordered autophagy-related proteins in various intra-nuclear organelles, such as the nucleolus, chromatin, Cajal bodies, nuclear speckles, promyelocytic leukemia (PML) nuclear bodies, nuclear lamina, nuclear pores, and perinucleolar compartment...
August 16, 2016: Molecular BioSystems
https://www.readbyqxmd.com/read/27307636/dflpred-high-throughput-prediction-of-disordered-flexible-linker-regions-in-protein-sequences
#5
Fanchi Meng, Lukasz Kurgan
MOTIVATION: Disordered flexible linkers (DFLs) are disordered regions that serve as flexible linkers/spacers in multi-domain proteins or between structured constituents in domains. They are different from flexible linkers/residues because they are disordered and longer. Availability of experimentally annotated DFLs provides an opportunity to build high-throughput computational predictors of these regions from protein sequences. To date, there are no computational methods that directly predict DFLs and they can be found only indirectly by filtering predicted flexible residues with predictions of disorder...
June 15, 2016: Bioinformatics
https://www.readbyqxmd.com/read/27044036/psionplus-accurate-sequence-based-predictor-of-ion-channels-and-their-types
#6
Jianzhao Gao, Wei Cui, Yajun Sheng, Jishou Ruan, Lukasz Kurgan
Ion channels are a class of membrane proteins that attracts a significant amount of basic research, also being potential drug targets. High-throughput identification of these channels is hampered by the low levels of availability of their structures and an observation that use of sequence similarity offers limited predictive quality. Consequently, several machine learning predictors of ion channels from protein sequences that do not rely on high sequence similarity were developed. However, only one of these methods offers a wide scope by predicting ion channels, their types and four major subtypes of the voltage-gated channels...
2016: PloS One
https://www.readbyqxmd.com/read/27037624/disordered-nucleiome-abundance-of-intrinsic-disorder-in-the-dna-and-rna-binding-proteins-in-1121-species-from-eukaryota-bacteria-and-archaea
#7
Chen Wang, Vladimir N Uversky, Lukasz Kurgan
Intrinsically disordered proteins (IDPs) are abundant in various proteomes, where they play numerous important roles and complement biological activities of ordered proteins. Among functions assigned to IDPs are interactions with nucleic acids. However, often, such assignments are made based on the guilty-by-association principle. The validity of the extension of these correlations to all nucleic acid binding proteins has never been analyzed on a large scale across all domains of life. To fill this gap, we perform a comprehensive computational analysis of the abundance of intrinsic disorder and intrinsically disordered domains in nucleiomes (∼548 000 nucleic acid binding proteins) of 1121 species from Archaea, Bacteria and Eukaryota...
May 2016: Proteomics
https://www.readbyqxmd.com/read/26712748/compartmentalization-and-functionality-of-nuclear-disorder-intrinsic-disorder-and-protein-protein-interactions-in-intra-nuclear-compartments
#8
Fanchi Meng, Insung Na, Lukasz Kurgan, Vladimir N Uversky
The cell nucleus contains a number of membrane-less organelles or intra-nuclear compartments. These compartments are dynamic structures representing liquid-droplet phases which are only slightly denser than the bulk intra-nuclear fluid. They possess different functions, have diverse morphologies, and are typically composed of RNA (or, in some cases, DNA) and proteins. We analyzed 3005 mouse proteins localized in specific intra-nuclear organelles, such as nucleolus, chromatin, Cajal bodies, nuclear speckles, promyelocytic leukemia (PML) nuclear bodies, nuclear lamina, nuclear pores, and perinuclear compartment and compared them with ~29,863 non-nuclear proteins from mouse proteome...
December 25, 2015: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/26651072/molecular-recognition-features-morfs-in-three-domains-of-life
#9
Jing Yan, A Keith Dunker, Vladimir N Uversky, Lukasz Kurgan
Intrinsically disordered proteins and protein regions offer numerous advantages in the context of protein-protein interactions when compared to the structured proteins and domains. These advantages include ability to interact with multiple partners, to fold into different conformations when bound to different partners, and to undergo disorder-to-order transitions concomitant with their functional activity. Molecular recognition features (MoRFs) are widespread elements located in disordered regions that undergo disorder-to-order transition upon binding to their protein partners...
March 2016: Molecular BioSystems
https://www.readbyqxmd.com/read/26504143/pdid-database-of-molecular-level-putative-protein-drug-interactions-in-the-structural-human-proteome
#10
Chen Wang, Gang Hu, Kui Wang, Michal Brylinski, Lei Xie, Lukasz Kurgan
MOTIVATION: Many drugs interact with numerous proteins besides their intended therapeutic targets and a substantial portion of these interactions is yet to be elucidated. Protein-Drug Interaction Database (PDID) addresses incompleteness of these data by providing access to putative protein-drug interactions that cover the entire structural human proteome. RESULTS: PDID covers 9652 structures from 3746 proteins and houses 16 800 putative interactions generated from close to 1...
February 15, 2016: Bioinformatics
https://www.readbyqxmd.com/read/26484121/genome-wide-analysis-of-thapsigargin-induced-micrornas-and-their-targets-in-nih3t3-cells
#11
Jody Groenendyk, Xiao Fan, Zhenling Peng, Yaroslav Ilnytskyy, Lukasz Kurgan, Marek Michalak
Disruption of the endoplasmic reticulum (ER) homeostasis is the cause of ER stress. We performed microRNA (miRNA) analysis (deep sequencing) to search for coping responses (including signaling pathways) induced by disrupted ER Ca(2 +) homeostasis. Our focus was on a specific branch of UPR namely the bi-functional protein kinase/endoribonuclease inositol-requiring element 1α (IRE1α). Activated IRE1α undergoes autophosphorylation and oligomerization, leading to the activation of the endoribonuclease domain and splicing of the mRNA encoding XBP1 specific transcription factor...
December 2014: Genomics Data
https://www.readbyqxmd.com/read/26297830/in-various-protein-complexes-disordered-protomers-have-large-per-residue-surface-areas-and-area-of-protein-dna-and-rna-binding-interfaces
#12
Zhonghua Wu, Gang Hu, Jianyi Yang, Zhenling Peng, Vladimir N Uversky, Lukasz Kurgan
We provide first large scale analysis of the peculiarities of surface areas of 5658 dissimilar (below 50% sequence similarity) proteins with known 3D-structures that bind to proteins, DNA or RNAs. We show here that area of the protein surface is highly correlated with the protein length. The size of the interface surface is only modestly correlated with the protein size, except for RNA-binding proteins where larger proteins are characterized by larger interfaces. Disordered proteins with disordered interfaces are characterized by significantly larger per-residue areas of their surfaces and interfaces when compared to the structured proteins...
September 14, 2015: FEBS Letters
https://www.readbyqxmd.com/read/26201486/untapped-potential-of-disordered-proteins-in-current-druggable-human-proteome
#13
REVIEW
Gang Hu, Zhonghua Wu, Kui Wang, Vladimir N Uversky, Lukasz Kurgan
Current efforts in design and characterization of drugs often rely on the structure of their protein targets. However, a large fraction of proteins lack unique 3-D structures and exist as highly dynamic structural ensembles. These intrinsically disordered proteins are involved in pathogenesis of various human diseases and are highly abundant in eukaryotes. Based on a comprehensive analysis of the current druggable human proteome covering 12 drug classes and 18 major classes of drug targets we show a significant bias toward high structural coverage and low abundance of intrinsic disorder...
2016: Current Drug Targets
https://www.readbyqxmd.com/read/26109352/high-throughput-prediction-of-rna-dna-and-protein-binding-regions-mediated-by-intrinsic-disorder
#14
Zhenling Peng, Lukasz Kurgan
Intrinsically disordered proteins and regions (IDPs and IDRs) lack stable 3D structure under physiological conditions in-vitro, are common in eukaryotes, and facilitate interactions with RNA, DNA and proteins. Current methods for prediction of IDPs and IDRs do not provide insights into their functions, except for a handful of methods that address predictions of protein-binding regions. We report first-of-its-kind computational method DisoRDPbind for high-throughput prediction of RNA, DNA and protein binding residues located in IDRs from protein sequences...
October 15, 2015: Nucleic Acids Research
https://www.readbyqxmd.com/read/26096987/unstructural-biology-of-the-dengue-virus-proteins
#15
Fanchi Meng, Reaid A Badierah, Hussein A Almehdar, Elrashdy M Redwan, Lukasz Kurgan, Vladimir N Uversky
In this study, we used a wide spectrum of bioinformatics techniques to evaluate the extent of intrinsic disorder in the complete proteomes of genotypes of four human dengue virus (DENV), to analyze the peculiarities of disorder distribution within individual DENV proteins, and to establish potential roles for the structural disorder with respect to their functions. We show that several proteins (ER, E, 1, 2A and 4A) are predicted to be mostly ordered, whereas four proteins (C, 2k, NS3 and NS5) are expected to have high disorder levels...
September 2015: FEBS Journal
https://www.readbyqxmd.com/read/25935161/a-comprehensive-comparative-review-of-sequence-based-predictors-of-dna-and-rna-binding-residues
#16
REVIEW
Jing Yan, Stefanie Friedrich, Lukasz Kurgan
Motivated by the pressing need to characterize protein-DNA and protein-RNA interactions on large scale, we review a comprehensive set of 30 computational methods for high-throughput prediction of RNA- or DNA-binding residues from protein sequences. We summarize these predictors from several significant perspectives including their design, outputs and availability. We perform empirical assessment of methods that offer web servers using a new benchmark data set characterized by a more complete annotation that includes binding residues transferred from the same or similar proteins...
January 2016: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/25935117/systematic-investigation-of-sequence-and-structural-motifs-that-recognize-atp
#17
Ke Chen, Dacheng Wang, Lukasz Kurgan
Interaction between ATP, a multifunctional and ubiquitous nucleotide, and proteins initializes phosphorylation, polypeptide synthesis and ATP hydrolysis which supplies energy for metabolism. However, current knowledge concerning the mechanisms through which ATP is recognized by proteins is incomplete, scattered, and inaccurate. We systemically investigate sequence and structural motifs of proteins that recognize ATP. We identified three novel motifs and refined the known p-loop and class II aminoacyl-tRNA synthetase motifs...
June 2015: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/25811425/correction-to-disordered-proteinaceous-machines
#18
Monika Fuxreiter, Ágnes Tóth-Petróczy, Daniel A Kraut, Andreas Matouschek, Roderick Y H Lim, Bin Xue, Lukasz Kurgan, Vladimir N Uversky
No abstract text is available yet for this article.
April 8, 2015: Chemical Reviews
https://www.readbyqxmd.com/read/25471818/comprehensive-overview-and-assessment-of-computational-prediction-of-microrna-targets-in-animals
#19
REVIEW
Xiao Fan, Lukasz Kurgan
MicroRNAs (miRNAs) are short endogenous noncoding RNAs that bind to target mRNAs, usually resulting in degradation and translational repression. Identification of miRNA targets is crucial for deciphering functional roles of the numerous miRNAs that are rapidly generated by sequencing efforts. Computational prediction methods are widely used for high-throughput generation of putative miRNA targets. We review a comprehensive collection of 38 miRNA sequence-based computational target predictors in animals that were developed over the past decade...
September 2015: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/25372670/covering-complete-proteomes-with-x-ray-structures-a-current-snapshot
#20
Marcin J Mizianty, Xiao Fan, Jing Yan, Eric Chalmers, Christopher Woloschuk, Andrzej Joachimiak, Lukasz Kurgan
Structural genomics programs have developed and applied structure-determination pipelines to a wide range of protein targets, facilitating the visualization of macromolecular interactions and the understanding of their molecular and biochemical functions. The fundamental question of whether three-dimensional structures of all proteins and all functional annotations can be determined using X-ray crystallography is investigated. A first-of-its-kind large-scale analysis of crystallization propensity for all proteins encoded in 1953 fully sequenced genomes was performed...
November 2014: Acta Crystallographica. Section D, Biological Crystallography
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