scholarly journals The Role of a Key Amino Acid Position in Species-Specific Proteinaceous dUTPase Inhibition

Biomolecules ◽  
2019 ◽  
Vol 9 (6) ◽  
pp. 221 ◽  
Author(s):  
András Benedek ◽  
Fanni Temesváry-Kis ◽  
Tamjidmaa Khatanbaatar ◽  
Ibolya Leveles ◽  
Éva Viola Surányi ◽  
...  
Keyword(s):  
Amino Acid ◽  
3D Structure ◽  
Three Dimensional ◽  
Amino Acid Position ◽  
Terminal Segment ◽  
Inhibition Mechanism ◽  
Structural Explanation ◽  
E Coli ◽  
Repair Enzymes ◽  
Species Specific

Protein inhibitors of key DNA repair enzymes play an important role in deciphering physiological pathways responsible for genome integrity, and may also be exploited in biomedical research. The staphylococcal repressor StlSaPIbov1 protein was described to be an efficient inhibitor of dUTPase homologues showing a certain degree of species-specificity. In order to provide insight into the inhibition mechanism, in the present study we investigated the interaction of StlSaPIbov1 and Escherichia coli dUTPase. Although we observed a strong interaction of these proteins, unexpectedly the E. coli dUTPase was not inhibited. Seeking a structural explanation for this phenomenon, we identified a key amino acid position where specific mutations sensitized E. coli dUTPase to StlSaPIbov1 inhibition. We solved the three-dimensional (3D) crystal structure of such a mutant in complex with the substrate analogue dUPNPP and surprisingly found that the C-terminal arm of the enzyme, containing the P-loop-like motif was ordered in the structure. This segment was never localized before in any other E. coli dUTPase crystal structures. The 3D structure in agreement with solution phase experiments suggested that ordering of the flexible C-terminal segment upon substrate binding is a major factor in defining the sensitivity of E. coli dUTPase for StlSaPIbov1 inhibition.

scholarly journals Neutralizing Epitopes and Residues Mediating the Potential Antigenic Drift of the Hemagglutinin-Esterase Protein of Influenza C Virus

Viruses ◽  
2018 ◽  
Vol 10 (8) ◽  
pp. 417 ◽  
Author(s):  
Yoko Matsuzaki ◽  
Kanetsu Sugawara ◽  
Yuki Furuse ◽  
Yoshitaka Shimotai ◽  
Seiji Hongo ◽  
...  
Keyword(s):  
Amino Acid ◽  
3D Structure ◽  
Three Dimensional ◽  
Antigenic Site ◽  
Antigenic Drift ◽  
Receptor Binding Site ◽  
Ann Arbor ◽  
Influenza C Virus ◽  
Escape Mutants ◽  
Antigenic Epitopes

We mapped the hemagglutinin-esterase (HE) antigenic epitopes of the influenza C virus on the three-dimensional (3D) structure of the HE glycoprotein using 246 escape mutants that were selected by a panel of nine anti-HE monoclonal antibodies (MAbs), including seven of the C/Ann Arbor/1/50 virus and two of the C/Yamagata/15/2004 virus. The frequency of variant selection in the presence of anti-HE MAbs was very low, with frequencies ranging from 10−4.62 to 10−7.58 for the C/Ann Arbor/1/50 virus and from 10−7.11 to 10−9.25 for the C/Yamagata/15/2004 virus. Sequencing of mutant HE genes revealed 25 amino acid substitutions at 16 positions in three antigenic sites: A-1, A-2, and A-3, and a newly designated Y-1 site. In the 3D structure, the A-1 site was widely located around the receptor-binding site, the A-2 site was near the receptor-destroying enzyme site, and the Y-1 site was located in the loop on the topside of HE. The hemagglutination inhibition reactions of the MAbs with influenza C viruses, circulating between 1947 and 2016, were consistent with the antigenic-site amino acid changes. We also found some amino acid variations in the antigenic site of recently circulating strains with antigenic changes, suggesting that viruses that have the potential to alter antigenicity continue to circulate in humans.

scholarly journals Amino Acids Sequence Based in Silico Analysis of RuBisCO (Ribulose-1,5 Bisphosphate Carboxylase Oxygenase) Proteins in Some Carthamus L. ssp.

2017 ◽  
Vol 9 (2) ◽  
pp. 204-208 ◽  
Author(s):  
Emre SEVİNDİK
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Average Length ◽  
3D Structure ◽  
Three Dimensional ◽  
In Silico Analysis ◽  
Bisphosphate Carboxylase ◽  
Molecular Weights ◽  
Acid Ratio ◽  
Important Enzyme

RuBisCO is an important enzyme for plants to photosynthesize and balance carbon dioxide in the atmosphere. This study aimed to perform sequence, physicochemical, phylogenetic and 3D (three-dimensional) comparative analyses of RuBisCO proteins in the Carthamus ssp. using various bioinformatics tools. The sequence lengths of the RuBisCO proteins were between 166 and 477 amino acids, with an average length of 411.8 amino acids. Their molecular weights (Mw) ranged from 18711.47 to 52843.09 Da; the most acidic and basic protein sequences were detected in C. tinctorius (pI = 5.99) and in C. tenuis (pI = 6.92), respectively. The extinction coefficients of RuBisCO proteins at 280 nm ranged from 17,670 to 69,830 M-1 cm-1, the instability index (II) values for RuBisCO proteins ranged from 33.31 to 39.39, while the GRAVY values of RuBisCO proteins ranged from -0.313 to -0.250. The most abundant amino acid in the RuBisCO protein was Gly (9.7%), while the least amino acid ratio was Trp (1.6 %). The putative phosphorylation sites of RuBisCO proteins were determined by NetPhos 2.0. Phylogenetic analysis revealed that RuBisCO proteins formed two main clades. A RAMPAGE analysis revealed that 96.3%-97.6% of residues were located in the favoured region of RuBisCO proteins. To predict the three dimensional (3D) structure of the RuBisCO proteins PyMOL was used. The results of the current study provide insights into fundamental characteristic of RuBisCO proteins in Carthamus ssp.

scholarly journals An in silico structural insights into Plasmodium LytB protein and its inhibition

2014 ◽  
Vol 70 (a1) ◽  
pp. C1791-C1791
Author(s):  
Rajabrata Bhunya ◽  
Suman Nandy ◽  
Alpana Seal
Keyword(s):  
In Silico ◽  
3D Structure ◽  
Three Dimensional ◽  
Comparative Modeling ◽  
Binding Energies ◽  
E Coli ◽  
Dimethylallyl Diphosphate ◽  
In Silico Study ◽  
Structural Insights ◽  
Insight Into

In most of the pathogenic organisms including Plasmodium falciparum, isoprenoids are synthesized via MEP (MethylErythritol 4-Phosphate) pathway. LytB is the last enzyme of this pathway which catalyzes the conversion of (E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate (HMBPP) into the two isoprenoid precursors: isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). Since the MEP pathway is not used by humans, it represents an attractive target for the development of new antimalarial compounds or inhibitors. Here a systematic in-silico study has been conducted to get an insight into the structure of Plasmodium lytB as well as its affinities towards different inhibitors. We used comparative modeling technique to predict the three dimensional (3D) structure of Plasmodium LytB taking E. Coli LytB protein (PDB ID: 3KE8) as template and the model was subsequently refined through molecular dynamics (MD) simulation. A large ligand dataset containing diphospate group was subjected for virtual screening against the target using GOLD 5.2 program. Considering the mode of binding and affinities, 17 leads were selected on basis of binding energies in comparison to its substrate HMBPP (Gold.Chemscore.DG: -20.9734 kcal/mol). Among them, 5 were discarded because of their inhibitory activity towards other human enzymes. The rest 12 potential leads carry all the properties of any "drug like" molecule and the knowledge of Plasmodium LytB inhibitory mechanism which can provide valuable support for the antimalarial inhibitor design in future.

scholarly journals Molecular Analysis of the Multiple GroEL Proteins of Chlamydiae

2003 ◽  
Vol 185 (6) ◽  
pp. 1958-1966 ◽  
Author(s):  
Karuna P. Karunakaran ◽  
Yasuyuki Noguchi ◽  
Timothy D. Read ◽  
Artem Cherkasov ◽  
Jeffrey Kwee ◽  
...  
Keyword(s):  
Amino Acid ◽  
Polyclonal Antibodies ◽  
Three Dimensional ◽  
Amino Acid Sequences ◽  
Developmental Cycle ◽  
Temperature Sensitive ◽  
Amino Acid Residues ◽  
E Coli ◽  
Chaperonin Groel ◽  
Mutant Complementation

ABSTRACT Genome sequencing revealed that all six chlamydiae genomes contain three groEL-like genes (groEL1, groEL2, and groEL3). Phylogenetic analysis of groEL1, groEL2, and groEL3 indicates that these genes are likely to have been present in chlamydiae since the beginning of the lineage. Comparison of deduced amino acid sequences of the three groEL genes with those of other organisms showed high homology only for groEL1, although comparison of critical amino acid residues that are required for polypeptide binding of the Escherichia coli chaperonin GroEL revealed substantial conservation in all three chlamydial GroELs. This was further supported by three-dimensional structural predictions. All three genes are expressed constitutively throughout the developmental cycle of Chlamydia trachomatis, although groEL1 is expressed at much higher levels than are groEL2 and groEL3. Transcription of groEL1, but not groEL2 and groEL3, was elevated when HeLa cells infected with C. trachomatis were subjected to heat shock. Western blot analysis with polyclonal antibodies raised against recombinant GroEL1, GroEL2, and GroEL3 demonstrated the presence of the three proteins in C. trachomatis elementary bodies, with GroEL1 being present in the largest amount. Only C. trachomatis groEL1 and groES together complemented a temperature-sensitive E. coli groEL mutant. Complementation did not occur with groEL2 or groEL3 alone or together with groES. The role for each of the three GroELs in the chlamydial developmental cycle and in disease pathogenesis requires further study.

scholarly journals Delta plus variant with neutral mutation is less virulent compared to wild type SARS-CoV2

2021 ◽  
Author(s):  
Sonal Upadhyay ◽  
Anuj Kumar ◽  
Pradeep Kumar ◽  
Pawan K. Dubey ◽  
Anima Tripathi ◽  
...  
Keyword(s):  
Protein Structure ◽  
Amino Acid ◽  
3D Structure ◽  
Amino Acid Position ◽  
Docking Study ◽  
Docking Studies ◽  
Wild Type ◽  
Neutral Mutation ◽  
New Variant ◽  
Antigen Antibody

Abstract BackgroundWith the start of the Coronavirus disease19 (COVID19) pandemic, the Coronavirus has mutated constantly. Recently a new variant called Delta plus has been reported in few countries, including South Africa, Brazil and India. The Delta plus variant contains an additional mutation called K417N on the coronavirus spike. The present study aims to determine the virulence and transmissibility of the Delta plus variant and to check the efficiency of different antibodies on its neutralization.Materials and MethodsDifferent computational tools such as PROVEAN, an online tool, HOPE server, simulation using CABS Flex, Clus pro, an online docking tool, were used to predict the structure and function of Delta plus variant by performing a comparative study with wild type protein. Also, to find an effective antibody against Delta plus variant, antigen-antibody docking studies were conducted through Clus pro server. Furthermore, we performed a 2D interaction diagram analysis to find the amino acid residue's interaction against antibodies.Results PROVEAN and HOPE showed the mutation (K417N) in the S-glycoprotein of Delta plus as NEUTRAL mutation. This mutation causes the loss of cysteine bonds leading to the destabilization of the 3D structure of spike protein. Furthermore, the RMSF plot emphasizing the 17th amino acid position of wild and Delta plus mutant revealed the high fluctuation of mutant protein structure compared to the wild protein structure. Further, a comparative docking study against hACE2 shows higher binding energy of wild-type RBD (-751.7 kcal/mol) than mutant RBD (-750.1 kcal/mol). Moreover, antigen-antibody docking study revealed higher affinity of BD-23 Fab antibodies with greater interaction energy ( -997 kcal/mol) compared to other antibodies and thus may prove to be a promising therapeutic against Delta plus variant.ConclusionDelta plus variant is less stable, has a lower binding affinity to hACE2 and has less virulence than wild type. However, the BD-23 Fab antibody has shown a more significant association for this variant and can be used in its treatment.

Search for conserved amino acid residues of the α-crystallin proteins of vertebrates

2016 ◽  
Vol 14 (02) ◽  
pp. 1641004 ◽  
Author(s):  
Nikita G. Shiliaev ◽  
Olga M. Selivanova ◽  
Oxana V. Galzitskaya
Keyword(s):  
Amino Acid ◽  
Bioinformatics Analysis ◽  
3D Structure ◽  
Three Dimensional ◽  
Aromatic Amino Acids ◽  
Small Heat Shock Protein ◽  
Lens Protein ◽  
Individual Amino Acid ◽  
Amino Acid Residues ◽  
Eye Lens Protein

[Formula: see text]-crystallin is the major eye lens protein and a member of the small heat-shock protein (sHsp) family. [Formula: see text]-crystallins have been shown to support lens clarity by preventing the aggregation of lens proteins. We performed the bioinformatics analysis of [Formula: see text]-crystallin sequences from vertebrates to find conserved amino acid residues as the three-dimensional (3D) structure of [Formula: see text]-crystallin is not identified yet. We are the first who demonstrated that the N-terminal region is conservative along with the central domain for vertebrate organisms. We have found that there is correlation between the conserved and structured regions. Moreover, amyloidogenic regions also correspond to the structured regions. We analyzed the amino acid composition of [Formula: see text]-crystallin A and B chains. Analyzing the occurrence of each individual amino acid residue, we have found that such amino acid residues as leucine, serine, lysine, proline, phenylalanine, histidine, isoleucine, glutamic acid, and valine change their content simultaneously in A and B chains in different classes of vertebrates. Aromatic amino acids occur more often in [Formula: see text]-crystallins from vertebrates than on the average in proteins among 17 animal proteomes. We obtained that the identity between A and B chains in the mammalian group is 0.35, which is lower than the published 0.60.

scholarly journals Identification of New Ocellatin Antimicrobial Peptides by cDNA Precursor Cloning in the Frame of This Family of Intriguing Peptides

Antibiotics ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 751
Author(s):  
Mariela M. Marani ◽  
Silvana Aguilar ◽  
Ana P. Cuzziol Boccioni ◽  
Natalia L. Cancelarich ◽  
Néstor G. Basso ◽  
...  
Keyword(s):  
Antimicrobial Activity ◽  
Amino Acid ◽  
Antimicrobial Peptides ◽  
In Silico ◽  
3D Structure ◽  
Three Dimensional ◽  
Amino Acid Residues ◽  
Conserved Residues ◽  
Α Helix ◽  
In Silico Analyses

Ocellatins are a family of antimicrobial peptides found exclusively in the Leptodactylus genus. To date, 10 species have been studied and more than 23 peptides described. Here we report the sequences of five new peptides from the skin of the frog Leptodactylus latrans (Anura: Leptodactylidae) determined by cDNA cloning of the complete prepro-peptide structures. The mature peptides were characterized with in silico tools and compared with those previously described. With 21 amino acid residues, this new set of peptides not previously described in the Leptodactylus genus share between 100 and 76.2% similarity to ocellatin antimicrobial peptides. These novel peptides are cationic and their three-dimensional (3D) structure holds the highly conserved residues G1, D4, K7, and K11 and a high theoretical amphipathic α-helix content. Furthermore, in silico analyses of these new peptides predicted antimicrobial activity. This study is framed in the context of previous work published about ocellatins, and therefore, provides a review of this intriguing family of peptides.

scholarly journals 3D structure of NT-3 Protein (Neurotropin 3) of Pigeon (Columba livia) using Server-Swiss Model

2021 ◽  
Vol 12 (2) ◽  
pp. 85
Author(s):  
Tina Zarkiyani ◽  
I Made Budiarsa ◽  
Astija Astija ◽  
Mursito S Bialangi
Keyword(s):  
Amino Acid ◽  
3D Structure ◽  
Three Dimensional ◽  
Columba Livia ◽  
Dimensional Structure ◽  
Structural Quality ◽  
Three Dimensional Structure ◽  
3 Dimensional ◽  
Access Code ◽  
Development And Differentiation

The NT-3 protein plays an important role in the development and differentiation of neurons, and is unique in the neurotropin family, that it can bind to 3 Trk receptors, namely TrkC, TrkA and TrkB. This study aimed to analyze the characteristics and three-dimensional structure of NT-3 protein in Columba livia. The target protein was obtained from Uniprot server with the access code of PKK30025.1 using template 3buk.1A (PDB-ID) analyzed in-silico through homology method using SWISS-MODEL server. The results showed that the three-dimensional structure of the target NT-3 protein with a template formed a β-sheet and loop structure, which was composed of 304 amino acids, with the highest amino acid composition was serine at 8.88 mol polar, and the lowest amino acid was tryptophan at 1.32. moles which was relatively nonpolar. The analysis results of the structural quality revealed an identity value of 98.20%, QMEAN of 0.8, QMQE of 0.25, and the analysis on the Ramachandran plot presented an outlier value of 0.92%; the most favored region value was 94.5%, with good structural quality. The results of the 3-dimensional structure of the NT-3 Columba livia protein are expected to be useful for further research to determine the active side and interactions of proteins in carrying out their functions.

3D reconstruction of the 50s ribosomal subunit of escherichia coli

1986 ◽  
Vol 44 ◽  
pp. 40-41
Author(s):  
M. Radermacher ◽  
T. Wagenknecht ◽  
A. Verschoor ◽  
J. Frank
Keyword(s):  
3D Reconstruction ◽  
3D Structure ◽  
Three Dimensional ◽  
Ribosomal Subunit ◽  
Main Body ◽  
Large Ribosomal Subunit ◽  
E Coli ◽  
Reconstruction Scheme ◽  
Particle Preparation ◽  
Electron Microscopical

The three-dimensional (3D) structure of the large ribosomal subunit from E. coli was determined from micrographs of a negatively stained 50S particle preparation using our new reconstruction scheme. The 50S subunit occurs in electron microscopical preparations mainly in the crown-view orientation with the interface side of the main body situated parallel to the specimen plane, but in random in plane orientations. An image of such a specimen tilted by a large tilt angle, which inherently contains a conical tilt series of the particle, was used to calculate a 3D reconstruction.

scholarly journals Direct coupling analysis improves the identification of beneficial amino acid mutations for the functional thermostabilization of a delicate decarboxylase

2019 ◽  
Vol 400 (11) ◽  
pp. 1519-1527 ◽  
Author(s):  
Martin Peng ◽  
Manfred Maier ◽  
Jan Esch ◽  
Alexander Schug ◽  
Kersten S. Rabe
Keyword(s):  
Amino Acid ◽  
Sequence Data ◽  
3D Structure ◽  
Three Dimensional ◽  
Computational Method ◽  
Single Amino Acid ◽  
Thiamine Pyrophosphate ◽  
Physical Parameters ◽  
Computer Based ◽  
Amino Acid Mutations

Abstract The optimization of enzyme properties for specific reaction conditions enables their tailored use in biotechnology. Predictions using established computer-based methods, however, remain challenging, especially regarding physical parameters such as thermostability without concurrent loss of activity. Employing established computational methods such as energy calculations using FoldX can lead to the identification of beneficial single amino acid substitutions for the thermostabilization of enzymes. However, these methods require a three-dimensional (3D)-structure of the enzyme. In contrast, coevolutionary analysis is a computational method, which is solely based on sequence data. To enable a comparison, we employed coevolutionary analysis together with structure-based approaches to identify mutations, which stabilize an enzyme while retaining its activity. As an example, we used the delicate dimeric, thiamine pyrophosphate dependent enzyme ketoisovalerate decarboxylase (Kivd) and experimentally determined its stability represented by a T50 value indicating the temperature where 50% of enzymatic activity remained after incubation for 10 min. Coevolutionary analysis suggested 12 beneficial mutations, which were not identified by previously established methods, out of which four mutations led to a functional Kivd with an increased T50 value of up to 3.9°C.

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