scholarly journals Zebra2: advanced and easy-to-use web-server for bioinformatic analysis of subfamily-specific and conserved positions in diverse protein superfamilies

2020 ◽  
Vol 48 (W1) ◽  
pp. W65-W71 ◽  
Author(s):  
Dmitry Suplatov ◽  
Yana Sharapova ◽  
Elizaveta Geraseva ◽  
Vytas Švedas
Keyword(s):  
Rational Design ◽  
Sequence Similarity ◽  
3D Structure ◽  
Web Server ◽  
Bioinformatic Analysis ◽  
Query Protein ◽  
Systematic Analysis ◽  
External Resources ◽  
Protein Superfamilies ◽  
Network Interfaces

Abstract Zebra2 is a highly automated web-tool to search for subfamily-specific and conserved positions (i.e. the determinants of functional diversity as well as the key catalytic and structural residues) in protein superfamilies. The bioinformatic analysis is facilitated by Mustguseal—a companion web-server to automatically collect and superimpose a large representative set of functionally diverse homologs with high structure similarity but low sequence identity to the selected query protein. The results are automatically prioritized and provided at four information levels to facilitate the knowledge-driven expert selection of the most promising positions on-line: as a sequence similarity network; interfaces to sequence-based and 3D-structure-based analysis of conservation and variability; and accompanied by the detailed annotation of proteins accumulated from the integrated databases with links to the external resources. The integration of Zebra2 and Mustguseal web-tools provides the first of its kind out-of-the-box open-access solution to conduct a systematic analysis of evolutionarily related proteins implementing different functions within a shared 3D-structure of the superfamily, determine common and specific patterns of function-associated local structural elements, assist to select hot-spots for rational design and to prepare focused libraries for directed evolution. The web-servers are free and open to all users at https://biokinet.belozersky.msu.ru/zebra2, no login required.

scholarly journals Molecular Characterization, Bioinformatic Analysis, and Expression Profile of Lin-28 Gene and Its Protein from Arabian Camel (Camelus dromedarius)

2019 ◽  
Vol 20 (9) ◽  
pp. 2291 ◽  
Author(s):  
Sultan N. Alharbi ◽  
Ibtehal S. Alduhaymi ◽  
Lama Alqahtani ◽  
Musaad A. Altammaami ◽  
Fahad M. Alhoshani ◽  
...  
Keyword(s):  
Structure Prediction ◽  
Rna Binding ◽  
Secondary Structure Prediction ◽  
Bos Taurus ◽  
Sequence Similarity ◽  
Zinc Fingers ◽  
3D Structure ◽  
Bioinformatic Analysis ◽  
Peptide Mass ◽  
Arabian Camel

Lin-28 is an RNA-binding protein that is known for its role in promoting the pluripotency of stem cells. In the present study, Arabian camel Lin-28 (cLin-28) cDNA was identified and analyzed. Full length cLin-28 mRNA was obtained using the reverse transcription polymerase chain reaction (RT-PCR). It was shown to be 715 bp in length, and the open reading frame (ORF) encoded 205 amino acids. The molecular weight and theoretical isoelectric point (pI) of the cLin-28 protein were predicted to be 22.389 kDa and 8.50, respectively. Results from the bioinformatics analysis revealed that cLin-28 has two main domains: an N-terminal cold-shock domain (CSD) and a C-terminal pair of retroviral-type Cysteine3Histidine (CCHC) zinc fingers. Sequence similarity and phylogenetic analysis showed that the cLin-28 protein is grouped together Camelus bactrianus and Bos taurus. Quantitative real-time PCR (qPCR) analysis showed that cLin-28 mRNA is highly expressed in the lung, heart, liver, and esophageal tissues. Peptide mass fingerprint-mass spectrometry (PMF-MS) analysis of the purified cLin-28 protein confirmed the identity of this protein. Comparing the modeled 3D structure of cLin-28 protein with the available protein 3D structure of the human Lin-28 protein confirmed the presence of CSD and retroviral-type CCHC zinc fingers, and high similarities were noted between the two structures by using super secondary structure prediction.

scholarly journals FoldRate: A Web-Server for Predicting Protein Folding Rates from Primary Sequence

2009 ◽  
Vol 3 (1) ◽  
pp. 31-50 ◽  
Author(s):  
Chou Kuo-Chen ◽  
Shen Hong-Bin
Keyword(s):  
3D Structure ◽  
Three Dimensional ◽  
Web Server ◽  
Query Protein ◽  
Sequence Information ◽  
Folding Rate ◽  
Structure Information ◽  
The Public ◽  
Folding Rates ◽  
User Friendly

With the avalanche of gene products in the postgenomic age, the gap between newly found protein sequences and the knowledge of their 3D (three dimensional) structures is becoming increasingly wide. It is highly desired to develop a method by which one can predict the folding rates of proteins based on their amino acid sequence information alone. To address this problem, an ensemble predictor, called FoldRate, was developed by fusing the folding-correlated features that can be either directly obtained or easily derived from the sequences of proteins. It was demonstrated by the jackknife cross-validation on a benchmark dataset constructed recently that FoldRate is at least comparable with or even better than the existing methods that, however, need both the sequence and 3D structure information for predicting the folding rate. As a user-friendly web-server, FoldRate is freely accessible to the public at www.csbio.sjtu.edu.cn/bioinf/FoldRate/, by which one can get the desired result for a query protein sequence in around 30 seconds.

scholarly journals Streptomonospora litoralis sp. nov., a halophilic thiopeptides producer isolated from sand collected at Cuxhaven beach

2021 ◽  
Author(s):  
Shadi Khodamoradi ◽  
Richard L. Hahnke ◽  
Yvonne Mast ◽  
Peter Schumann ◽  
Peter Kämpfer ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Bioinformatic Analysis ◽  
Biosynthetic Gene Cluster ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Polar Lipid Profile

AbstractStrain M2T was isolated from the beach of Cuxhaven, Wadden Sea, Germany, in course of a program to attain new producers of bioactive natural products. Strain M2T produces litoralimycin and sulfomycin-type thiopeptides. Bioinformatic analysis revealed a potential biosynthetic gene cluster encoding for the M2T thiopeptides. The strain is Gram-stain-positive, rod shaped, non-motile, spore forming, showing a yellow colony color and forms extensively branched substrate mycelium and aerial hyphae. Inferred from the 16S rRNA gene phylogeny strain M2T affiliates with the genus Streptomonospora. It shows 96.6% 16S rRNA gene sequence similarity to the type species Streptomonospora salina DSM 44593 T and forms a distinct branch with Streptomonospora sediminis DSM 45723 T with 97.0% 16S rRNA gene sequence similarity. Genome-based phylogenetic analysis revealed that M2T is closely related to Streptomonospora alba YIM 90003 T with a digital DNA-DNA hybridisation (dDDH) value of 26.6%. The predominant menaquinones of M2T are MK-10(H6), MK-10(H8), and MK-11(H6) (> 10%). Major cellular fatty acids are iso-C16:0, anteiso C17:0 and C18:0 10-methyl. The polar lipid profile consisted of diphosphatidylglycerol phosphatidyl glycerol, phosphatidylinositol, phosphatidylcholine, phosphatidylethanolamine, three glycolipids, two unknown phospholipids, and two unknown lipids. The genome size of type strain M2T is 5,878,427 bp with 72.1 mol % G + C content. Based on the results obtained from phylogenetic and chemotaxonomic studies, strain M2T (= DSM 106425 T = NCCB 100650 T) is considered to represent a novel species within the genus Streptomonospora for which the name Streptomonospora litoralis sp. nov. is proposed.

scholarly journals Fluorescent thermal shift-based method for detection of NF-κB binding to double-stranded DNA

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Peter D. Leitner ◽  
Ilja Vietor ◽  
Lukas A. Huber ◽  
Taras Valovka
Keyword(s):  
Dna Binding ◽  
Rational Design ◽  
Dissociation Constants ◽  
Inflammatory Diseases ◽  
Dimethyl Fumarate ◽  
Bioinformatic Analysis ◽  
Quantitative Detection ◽  
Regulatory Sequences ◽  
Wide Range ◽  
Inhibitory Drug

AbstractThe nuclear factor kappa B (NF-κB) family of dimeric transcription factors regulates a wide range of genes by binding to their specific DNA regulatory sequences. NF-κB is an important therapeutic target linked to a number of cancers as well as autoimmune and inflammatory diseases. Therefore, effective high-throughput methods for the detection of NF-κB DNA binding are essential for studying its transcriptional activity and for inhibitory drug screening. We describe here a novel fluorescence-based assay for quantitative detection of κB consensus double-stranded (ds) DNA binding by measuring the thermal stability of the NF-κB proteins. Specifically, DNA binding proficient NF-κB probes, consisting of the N-terminal p65/RelA (aa 1–306) and p50 (aa 1–367) regions, were designed using bioinformatic analysis of protein hydrophobicity, folding and sequence similarities. By measuring the SYPRO Orange fluorescence during thermal denaturation of the probes, we detected and quantified a shift in the melting temperatures (ΔTm) of p65/RelA and p50 produced by the dsDNA binding. The increase in Tm was proportional to the concentration of dsDNA with apparent dissociation constants (KD) of 2.228 × 10–6 M and 0.794 × 10–6 M, respectively. The use of withaferin A (WFA), dimethyl fumarate (DMF) and p-xyleneselenocyanate (p-XSC) verified the suitability of this assay for measuring dose-dependent antagonistic effects on DNA binding. In addition, the assay can be used to analyse the direct binding of inhibitors and their effects on structural stability of the protein probe. This may facilitate the identification and rational design of new drug candidates interfering with NF-κB functions.

scholarly journals Structure of SPH (self-incompatibility protein homologue) proteins: a widespread family of small, highly stable, secreted proteins

2019 ◽  
Vol 476 (5) ◽  
pp. 809-826
Author(s):  
Karthik V. Rajasekar ◽  
Shuangxi Ji ◽  
Rachel J. Coulthard ◽  
Jon P. Ride ◽  
Gillian L. Reynolds ◽  
...  
Keyword(s):  
Fusion Protein ◽  
Analytical Ultracentrifugation ◽  
De Novo ◽  
Learning Algorithm ◽  
Sequence Similarity ◽  
Homology Modelling ◽  
3D Structure ◽  
Large Family ◽  
Secreted Proteins ◽  
Self Incompatibility

Abstract SPH (self-incompatibility protein homologue) proteins are a large family of small, disulfide-bonded, secreted proteins, initially found in the self-incompatibility response in the field poppy (Papaver rhoeas), but now known to be widely distributed in plants, many containing multiple members of this protein family. Using the Origami strain of Escherichia coli, we expressed one member of this family, SPH15 from Arabidopsis thaliana, as a folded thioredoxin fusion protein and purified it from the cytosol. The fusion protein was cleaved and characterised by analytical ultracentrifugation, circular dichroism and nuclear magnetic resonance (NMR) spectroscopy. This showed that SPH15 is monomeric and temperature stable, with a β-sandwich structure. The four strands in each sheet have the same topology as the unrelated proteins: human transthyretin, bacterial TssJ and pneumolysin, with no discernible sequence similarity. The NMR-derived structure was compared with a de novo model, made using a new deep learning algorithm based on co-evolution/correlated mutations, DeepCDPred, validating the method. The DeepCDPred de novo method and homology modelling to SPH15 were then both used to derive models of the 3D structure of the three known PrsS proteins from P. rhoeas, which have only 15–18% sequence homology to SPH15. The DeepCDPred method gave models with lower discreet optimised protein energy scores than the homology models. Three loops at one end of the poppy structures are postulated to interact with their respective pollen receptors to instigate programmed cell death in pollen tubes.

scholarly journals Rational Design for Mn3O4@carbon Foam Nanocomposite with 0D@3D Structure for Boosting Electrochemical Performance

2020 ◽  
Author(s):  
Zhu Yihan ◽  
Dongfeng Wang ◽  
Xuehua Yan ◽  
Yanli Li ◽  
Wending Zhou ◽  
...  
Keyword(s):  
Electrochemical Performance ◽  
Current Density ◽  
Rational Design ◽  
Hydrothermal Reaction ◽  
3D Structure ◽  
Carbon Foam ◽  
Transfer Path ◽  
3D Architecture ◽  
One Step ◽  
Mn3o4 Nanoparticles

Abstract A rational strategy was developed to prepare a nanocomposite with 0D/3D architecture. The composite containing Mn3O4 nanoparticles (0D) and carbon foam (3D) could be applied as an electrode material for supercapacitor by taking advantage of high conductivity of carbon foam (CF) and high pseudocapacitance of Mn3O4 nanoparticles. CF was prepared by a carbonization method using melamine foam, and then Mn3O4 nanoparticles were combined with carbon foam by a one-step hydrothermal method to prepare Mn3O4@CF nanocomposite. The 0D@3D hierarchical structure of Mn3O4@CF nanocomposite using CF as a 3D growing skeleton prevents agglomeration and increases reactive sites of Mn3O4 nanoparticles. In addition, CF as a conductive skeleton shortens the charge transfer path. The synergistic effect between CF and Mn3O4 improves the electrochemical performance of CF. Three Mn3O4@CF composites were prepared by adjusting the mass of the reactants in the processes of hydrothermal reaction. The Mn3O4 nanoparticles are uniformly grown on the CF surface with a diameter of 18 nm. Mn3O4@CF-2 composite has a specific capacitance of 212.8 F/g at a current density of 1 A/g, which is much higher than that of pristine CF (79.1 F/g) and Mn3O4 (112.7 F/g). The cyclic stability of Mn3O4@CF-2 is retained as 86.1% of initial capacitance after 2000 cycles at the current density of 1 A/g. It proves the feasibility of the as-mentioned strategy and broadens the application of carbon foam in supercapacitor.

The visualCMAT: A web-server to select and interpret correlated mutations/co-evolving residues in protein families

2018 ◽  
Vol 16 (02) ◽  
pp. 1840005 ◽  
Author(s):  
Dmitry Suplatov ◽  
Yana Sharapova ◽  
Daria Timonina ◽  
Kirill Kopylov ◽  
Vytas Švedas
Keyword(s):  
Rational Design ◽  
Visual Analysis ◽  
Structural Information ◽  
Protein Structures ◽  
Web Server ◽  
Physical Contact ◽  
Protein Families ◽  
Sequence Alignments ◽  
Homologous Proteins ◽  
Correlated Mutations

The visualCMAT web-server was designed to assist experimental research in the fields of protein/enzyme biochemistry, protein engineering, and drug discovery by providing an intuitive and easy-to-use interface to the analysis of correlated mutations/co-evolving residues. Sequence and structural information describing homologous proteins are used to predict correlated substitutions by the Mutual information-based CMAT approach, classify them into spatially close co-evolving pairs, which either form a direct physical contact or interact with the same ligand (e.g. a substrate or a crystallographic water molecule), and long-range correlations, annotate and rank binding sites on the protein surface by the presence of statistically significant co-evolving positions. The results of the visualCMAT are organized for a convenient visual analysis and can be downloaded to a local computer as a content-rich all-in-one PyMol session file with multiple layers of annotation corresponding to bioinformatic, statistical and structural analyses of the predicted co-evolution, or further studied online using the built-in interactive analysis tools. The online interactivity is implemented in HTML5 and therefore neither plugins nor Java are required. The visualCMAT web-server is integrated with the Mustguseal web-server capable of constructing large structure-guided sequence alignments of protein families and superfamilies using all available information about their structures and sequences in public databases. The visualCMAT web-server can be used to understand the relationship between structure and function in proteins, implemented at selecting hotspots and compensatory mutations for rational design and directed evolution experiments to produce novel enzymes with improved properties, and employed at studying the mechanism of selective ligand’s binding and allosteric communication between topologically independent sites in protein structures. The web-server is freely available at https://biokinet.belozersky.msu.ru/visualcmat and there are no login requirements.

A Method of Structure Comparison Using Spatial Topological Patterns

2005 ◽  
Vol 277-279 ◽  
pp. 272-277
Author(s):  
Sung Hee Park ◽  
Keun Ho Ryu
Keyword(s):  
Spatial Data ◽  
Similarity Search ◽  
3D Structure ◽  
Structural Similarity ◽  
Query Protein ◽  
Data Types ◽  
Structure Comparison ◽  
3D Space ◽  
Structure Databases ◽  
Computationally Expensive

The problem of comparison of structural similarity has been complex and computationally expensive. The first step to solve comparison of structural similarity in 3D structure databases is to develop fast methods for structural similarity. Therefore, we propose a new method of comparing structural similarity in protein structure databases by using topological patterns of proteins. In our approach, the geometry of secondary structure elements in 3D space is represented by spatial data types and is indexed using Rtrees. Topological patterns are discovered by spatial topology relations based on the Rtree index join. An algorithm for a similarity search compares topological patterns of a query protein with those of proteins in structure databases by the intersection frequency of SSEs. Our experimental results show that the execution time of our method is three times faster than the generally known method DALITE. Our method can generate small candidate sets for more accurate alignment tools such as DALI and SSAP.

scholarly journals The cryoelectron microscopy structure of the human CDK-activating kinase

2020 ◽  
Vol 117 (37) ◽  
pp. 22849-22857 ◽  
Author(s):  
Basil J. Greber ◽  
Juan M. Perez-Bertoldi ◽  
Kif Lim ◽  
Anthony T. Iavarone ◽  
Daniel B. Toso ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Rna Polymerase Ii ◽  
Transcription Initiation ◽  
Rational Design ◽  
Control Cell ◽  
3D Structure ◽  
Structural Basis ◽  
Pol Ii ◽  
Insight Into ◽  
Cdk Activating Kinase

The human CDK-activating kinase (CAK), a complex composed of cyclin-dependent kinase (CDK) 7, cyclin H, and MAT1, is a critical regulator of transcription initiation and the cell cycle. It acts by phosphorylating the C-terminal heptapeptide repeat domain of the RNA polymerase II (Pol II) subunit RPB1, which is an important regulatory event in transcription initiation by Pol II, and it phosphorylates the regulatory T-loop of CDKs that control cell cycle progression. Here, we have determined the three-dimensional (3D) structure of the catalytic module of human CAK, revealing the structural basis of its assembly and providing insight into CDK7 activation in this context. The unique third component of the complex, MAT1, substantially extends the interaction interface between CDK7 and cyclin H, explaining its role as a CAK assembly factor, and it forms interactions with the CDK7 T-loop, which may contribute to enhancing CAK activity. We have also determined the structure of the CAK in complex with the covalently bound inhibitor THZ1 in order to provide insight into the binding of inhibitors at the CDK7 active site and to aid in the rational design of therapeutic compounds.

scholarly journals New Insights on the Feature and Function of Tail Tubular Protein B and Tail Fiber Protein of the Lytic Bacteriophage φYeO3-12 Specific for Yersinia enterocolitica Serotype O:3

Molecules ◽  
2020 ◽  
Vol 25 (19) ◽  
pp. 4392
Author(s):  
Anna Pyra ◽  
Karolina Filik ◽  
Bożena Szermer-Olearnik ◽  
Anna Czarny ◽  
Ewa Brzozowska
Keyword(s):  
Yersinia Enterocolitica ◽  
3D Structure ◽  
Bioinformatic Analysis ◽  
Thermal Unfolding ◽  
Tail Fiber ◽  
Lytic Bacteriophage ◽  
Serotype O ◽  
Phage T7 ◽  
Domain Protein ◽  
Aggregation Temperature

For the first time, we are introducing TTPBgp12 and TFPgp17 as new members of the tail tubular proteins B (TTPB) and tail fiber proteins (TFP) family, respectively. These proteins originate from Yersinia enterocolitica phage φYeO3-12. It was originally thought that these were structural proteins. However, our results show that they also inhibit bacterial growth and biofilm formation. According to the bioinformatic analysis, TTPBgp12 is functionally and structurally similar to the TTP of Enterobacteria phage T7 and adopts a β-structure. TFPgp17 contains an intramolecular chaperone domain at its C-terminal end. The N-terminus of TFPgp17 is similar to other representatives of the TFP family. Interestingly, the predicted 3D structure of TFPgp17 is similar to other bacterial S-layer proteins. Based on the thermal unfolding experiment, TTPBgp12 seems to be a two-domain protein that aggregates in the presence of sugars such as maltose and N-acetylglucosamine (GlcNAc). These sugars cause two unfolding events to transition into one global event. TFPgp17 is a one-domain protein. Maltose and GlcNAc decrease the aggregation temperature of TFPgp17, while the presence of N-acetylgalactosamine (GalNAc) increases the temperature of its aggregation. The thermal unfolding analysis of the concentration gradient of TTPBgp12 and TFPgp17 indicates that with decreasing concentrations, both proteins increase in stability. However, a decrease in the protein concentration also causes an increase in its aggregation, for both TTPBgp12 and TFPgp17.

Sign in / Sign up

Export Citation Format

Share Document