scholarly journals Molecular Adaptations of Bacterial Mercuric Reductase to the Hypersaline Kebrit Deep in the Red Sea

2018 ◽  
Vol 85 (4) ◽  
Author(s):  
Eman Ramadan ◽  
Mohamad Maged ◽  
Ahmed El Hosseiny ◽  
Felipe S. Chambergo ◽  
João C. Setubal ◽  
...  
Keyword(s):  
Amino Acid ◽  
Red Sea ◽  
Compatible Solutes ◽  
Three Dimensional ◽  
Environmental Stressors ◽  
The Other ◽  
Dimensional Structure ◽  
Amino Acid Substitutions ◽  
Dependent Manner ◽  
Osmotic Balance

ABSTRACTThe hypersaline Kebrit Deep brine pool in the Red Sea is characterized by high levels of toxic heavy metals. Here, we describe two structurally related mercuric reductases (MerAs) from this site which were expressed inEscherichia coli. Sequence similarities suggest that both genes are derived from proteobacteria, most likely theBetaproteobacteriaorGammaproteobacteria. We show that one of the enzymes (K35NH) is strongly inhibited by NaCl, while the other (K09H) is activated in a NaCl-dependent manner. We infer from this difference that the two forms might support the detoxification of mercury in bacterial microorganisms that employ the compatible solutes and salt-in strategies, respectively. Three-dimensional structure modeling shows that all amino acid substitutions unique to each type are located outside the domain responsible for formation of the active MerA homodimer, and the vast majority of these are found on the surface of the molecule. Moreover, K09H exhibits the predominance of acidic over hydrophobic side chains that is typical of halophilic salt-dependent proteins. These findings enhance our understanding of how selection pressures imposed by two environmental stressors have endowed MerA enzymes with catalytic properties that can potentially function in microorganisms that utilize distinct mechanisms for osmotic balance in hypersaline environments.IMPORTANCEAnalysis of two structurally homologous but catalytically distinct mercuric reductases from the Kebrit Deep brine in the Red Sea sheds light on the adaptations that enable microorganisms to cope simultaneously with extreme salinity and toxic mercury compounds. One is strongly inhibited by high NaCl concentrations, while the other exhibits NaCl-dependent activation. Their different activity profiles imply that they may derive from bacterial microorganisms that utilize compatible solutes and salt-in strategies, respectively, to maintain osmotic balance. Three-dimensional modeling reveals that regions not involved in formation of the active homodimer are conserved between the two. However, in the NaCl-dependent form, distinct amino acid substitutions are found in areas that are critical for stability in high salt. The work provides insights into how two environmental stressors have shaped the structure of orthologous enzymes through selection and adaptation, enabling them to retain their catalytic function in what may be very different cellular contexts.

Polymorphism in the coding sequence of the horse transferrin gene

Genome ◽  
1994 ◽  
Vol 37 (1) ◽  
pp. 157-165 ◽  
Author(s):  
Margaret A. Carpenter ◽  
Tom E. Broad
Keyword(s):  
Amino Acid ◽  
Iron Transport ◽  
Nucleotide Substitution ◽  
Three Dimensional ◽  
Sequence Polymorphism ◽  
Dimensional Structure ◽  
Amino Acid Substitutions ◽  
Nucleotide Substitutions ◽  
Coding Sequence ◽  
Transferrin Gene

Transferrin, the iron transport protein of the blood, is highly polymorphic in many species, including the horse. A number of sequence polymorphisms that distinguish several of the variants of horse transferrin are reported here. Previous studies indicated that exons 12 and 15 were likely to be polymorphic. Sequencing regions of exons 12 and 15 from D and R variants revealed 10 nucleotide substitutions that encoded six amino acid replacements. The F1, F2, H2, and * variants were identical to D, and the O variant was almost identical to R, in the regions studied. The data indicated that the horse transferrin variants make up two distinct groups. The positions of differences between the D and F1 alleles were determined by analyzing single-stranded conformation polymorphisms. Sequencing then revealed three nucleotide substitutions, two of which encoded amino acid substitutions. Location of the eight polymorphic residues on the three-dimensional structure of human lactoferrin revealed that all were clustered at one end of the C-lobe.Key words: sequence polymorphism, transferrin, horse, nucleotide substitution, allele.

scholarly journals THE SENSITIVITY OF GEL ELECTROPHORESIS AS A DETECTOR OF GENETIC VARIATION

Genetics ◽  
1979 ◽  
Vol 93 (4) ◽  
pp. 1019-1037
Author(s):  
John A M Ramshaw ◽  
Jerry A Coyne ◽  
R C Lewontin
Keyword(s):  
Amino Acid ◽  
Gel Electrophoresis ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Amino Acid Substitutions ◽  
Substantial Fraction ◽  
Sequential Method ◽  
The Third ◽  
Protein Variation ◽  
Hemoglobin Variants

ABSTRACT Three experiments based on an idea of YOUDERIAN have been performed to determine the proportions and kinds of amino acid substitutions that are detected by gel electrophoresis when applied to surveys of protein variation in populations. The experiments involved applying the sequential method of electrophoresis under sereral conditions of pH and gel concentration to a large sample of human hemoglobins with known amino acid substitutions. In the first experiment, a random sample of 20 different hemoglobin variants was studied, and these were separated into 17 distinct electrophoretic classes by three sequential gel conditions, thus giving a detectability of 85%. A single pass under standard conditions detected eight classes. The second experiment compared groups of substitutions that were chemically identical, but in different positions in the α and β chains, while the third experiment compared pairs of substitutions that were charge equivalent. but chemically different at the same chain position. The sequential method distinguished 90% of all chemically identical substitutions when they were at different chain locations, and four out of five charge equivalent but chemically different substitutions at the same site. Examination of the location of each substitution in the three-dimensional structure of hemoglobins showed that interior substitutions usually are less different from HbA than are surface substitutions and that local interactions with chain and spatial neighbors are sufficient to distinguish substitutions in very similar positions on the outside of the molecule. The "charge ladder" model of electrophoretic classes is clearly incorrect, and it appears that sequential gel electrophoresis as practiced in our Drosophila surveys has detected a substantial fraction of amino acid substitutions if hemoglobin is regarded as a model. This estimate may be modified as other molecules beside hemoglobin are subjected to similar calibration experiments.

scholarly journals Biochemical features of parvovirus B19 genovariant 1a2 dominating during the incidence rise in Belarus

2020 ◽  
Vol 17 (2) ◽  
pp. 211-220
Author(s):  
M. A. Yermalovich ◽  
V. V. Khrustalev ◽  
T. A. Khrustaleva ◽  
V. V. Poboinev ◽  
E. O. Samoilovich
Keyword(s):  
Amino Acid ◽  
Parvovirus B19 ◽  
Three Dimensional ◽  
Amino Acid Sequences ◽  
Dimensional Structure ◽  
Amino Acid Substitutions ◽  
Structural Protein ◽  
Mutational Pressure ◽  
Amino Acid Variability ◽  
Unique Amino Acid

Two genovariants (1a1 and 1a2) are distinguished among Human parvovirus B19 (B19P) of subgenotype 1a, of which 1a2 was predominantly distributed during the incidence rise in Belarus. The aim of this study was a comparative analysis of the amino acid variability and of the mutational pressure directions in different parts of the genome between genovariants 1a1 and 1a2.The analysis of the consensus amino acid sequences of two genovariants and the three-dimensional structure models of protein fragments was carried out. In total, two unique amino acid substitutions in the main non-structural protein NS1 of 1a2 were found (I181M and E114G), one of which E114G is close to the DNA-binding domain (OBD) responsible for attachment to the replication origin site and can affect the rate of virus replication and transcription. Three unique amino acid substitutions were found in the structural polypeptide VP of 1a2: V30L, S98N, and N533S. Two of them are located in the most immunogenic region VP1u and can contribute to the escape from immune response. The investigation of the mutational pressure direction revealed a decrease in the frequency of G to T transversions in the second reading frame of 1a2, which reflects a higher transcription rate as a result of amino acid substitution in the OBD protein.The differences revealed between the genetic variants of subgenotype 1a B19P both in the antigenic sites and in the replication and transcription system can provide an increased “fitness” for the genetic variant 1a2 and explain its predominant distribution during the incidence rise.

scholarly journals Structural analysis of mutations in the Drosophila beta 2-tubulin isoform reveals regions in the beta-tubulin molecular required for general and for tissue-specific microtubule functions.

Genetics ◽  
1995 ◽  
Vol 139 (1) ◽  
pp. 267-286 ◽  
Author(s):  
J D Fackenthal ◽  
J A Hutchens ◽  
F R Turner ◽  
E C Raff
Keyword(s):  
Amino Acid ◽  
Three Dimensional ◽  
Variable Region ◽  
Internal Variable ◽  
Microtubule Assembly ◽  
Dimensional Structure ◽  
Wild Type ◽  
Beta Tubulin ◽  
Assembly Kinetics ◽  
Beta 2

Abstract We have determined the lesions in a number of mutant alleles of beta Tub85D, the gene that encodes the testis-specific beta 2-tubulin isoform in Drosophila melanogaster. Mutations responsible for different classes of functional phenotypes are distributed throughout the beta 2-tubulin molecule. There is a telling correlation between the degree of phylogenetic conservation of the altered residues and the number of different microtubule categories disrupted by the lesions. The majority of lesions occur at positions that are evolutionarily highly conserved in all beta-tubulins; these lesions disrupt general functions common to multiple classes of microtubules. However, a single allele B2t6 contains an amino acid substitution within an internal cluster of variable amino acids that has been identified as an isotype-defining domain in vertebrate beta-tubulins. Correspondingly, B2t6 disrupts only a subset of microtubule functions, resulting in misspecification of the morphology of the doublet microtubules of the sperm tail axoneme. We previously demonstrated that beta 3, a developmentally regulated Drosophila beta-tubulin isoform, confers the same restricted morphological phenotype in a dominant way when it is coexpressed in the testis with wild-type beta 2-tubulin. We show here by complementation analysis that beta 3 and the B2t6 product disrupt a common aspect of microtubule assembly. We therefore conclude that the amino acid sequence of the beta 2-tubulin internal variable region is required for generation of correct axoneme morphology but not for general microtubule functions. As we have previously reported, the beta 2-tubulin carboxy terminal isotype-defining domain is required for suprastructural organization of the axoneme. We demonstrate here that the beta 2 variant lacking the carboxy terminus and the B2t6 variant complement each other for mild-to-moderate meiotic defects but do not complement for proper axonemal morphology. Our results are consistent with the hypothesis drawn from comparisons of vertebrate beta-tubulins that the two isotype-defining domains interact in a three-dimensional structure in wild-type beta-tubulins. We propose that the integrity of this structure in the Drosophila testis beta 2-tubulin isoform is required for proper axoneme assembly but not necessarily for general microtubule functions. On the basis of our observations we present a model for regulation of axoneme microtubule morphology as a function of tubulin assembly kinetics.

A new three-dimensional anionic cadmium(II) dicyanamide network

2014 ◽  
Vol 70 (11) ◽  
pp. 1054-1056 ◽  
Author(s):  
Qiang Li ◽  
Hui-Ting Wang
Keyword(s):  
Crystal Structure ◽  
Aqueous Solution ◽  
Unit Cell Volume ◽  
Three Dimensional ◽  
Building Blocks ◽  
The Other ◽  
Dimensional Structure ◽  
Cadmium Nitrate ◽  
Nitrate Tetrahydrate ◽  
Anionic Framework

A new cadmium dicyanamide complex, poly[tetramethylphosphonium [μ-chlorido-di-μ-dicyanamido-κ4N1:N5-cadmium(II)]], [(CH3)4P][Cd(NCNCN)2Cl], was synthesized by the reaction of tetramethylphosphonium chloride, cadmium nitrate tetrahydrate and sodium dicyanamide in aqueous solution. In the crystal structure, each CdIIatom is octahedrally coordinated by four terminal N atoms from four anionic dicyanamide (dca) ligands and by two chloride ligands. The dicyanamide ligands play two different roles in the building up of the structure; one role results in the formation of [Cd(dca)Cl]2building blocks, while the other links the building blocks into a three-dimensional structure. The anionic framework exhibits a solvent-accessible void of 673.8 Å3, amounting to 47.44% of the total unit-cell volume. The cavities in the network are occupied by pairs of tetramethylphosphonium cations.

scholarly journals Bis(μ2-4-nitrophenolato)bis(4-nitrophenolato)di-μ3-oxido-octaphenyltetratin chloroform sesquisolvate [+ solvate]: a tetranuclear stannoxane

IUCrData ◽  
2019 ◽  
Vol 4 (8) ◽  
Author(s):  
Patrick Butler
Keyword(s):  
Hydrogen Bonds ◽  
Electron Density ◽  
Three Dimensional ◽  
The Other ◽  
Dimensional Structure ◽  
Coordination Geometry ◽  
Asymmetric Unit ◽  
Acta Cryst ◽  
Complex Molecules ◽  
Three Dimensional Structure

The title tetranuclear stannoxane, [Sn4(C6H5)8(C6H4NO3)4O2]·1.5CHCl3·solvent, crystallized with two independent complex molecules, A and B, in the asymmetric unit together with 1.5 molecules of chloroform. There is also a region of disordered electron density, which was corrected for using the SQUEEZE routine [Spek (2015). Acta Cryst. C71, 9–18]. The oxo-tin core of each complex is in a planar `ladder' arrangement and each Sn atom is fivefold SnO3C2 coordinated, with one tin centre having an almost perfect square-pyramidal coordination geometry, while the other three Sn centres have distorted shapes. In the crystal, the complex molecules are arranged in layers, composed of A or B complexes, lying parallel to the bc plane. The complex molecules are linked by a number of C—H...O hydrogen bonds within the layers and between the layers, forming a supramolecular three-dimensional structure.

scholarly journals Selection of sequence motifs and generative Hopfield-Potts models for protein families

2019 ◽  
Author(s):  
Kai Shimagaki ◽  
Martin Weigt
Keyword(s):  
Amino Acid ◽  
Ad Hoc ◽  
Three Dimensional ◽  
Generative Models ◽  
Amino Acid Sequences ◽  
Dimensional Structure ◽  
Sequence Motifs ◽  
Restricted Boltzmann Machines ◽  
Potts Models ◽  
Maximum Entropy Models

Statistical models for families of evolutionary related proteins have recently gained interest: in particular pairwise Potts models, as those inferred by the Direct-Coupling Analysis, have been able to extract information about the three-dimensional structure of folded proteins, and about the effect of amino-acid substitutions in proteins. These models are typically requested to reproduce the one- and two-point statistics of the amino-acid usage in a protein family, i.e. to capture the so-called residue conservation and covariation statistics of proteins of common evolutionary origin. Pairwise Potts models are the maximum-entropy models achieving this. While being successful, these models depend on huge numbers of ad hoc introduced parameters, which have to be estimated from finite amount of data and whose biophysical interpretation remains unclear. Here we propose an approach to parameter reduction, which is based on selecting collective sequence motifs. It naturally leads to the formulation of statistical sequence models in terms of Hopfield-Potts models. These models can be accurately inferred using a mapping to restricted Boltzmann machines and persistent contrastive divergence. We show that, when applied to protein data, even 20-40 patterns are sufficient to obtain statistically close-to-generative models. The Hopfield patterns form interpretable sequence motifs and may be used to clusterize amino-acid sequences into functional sub-families. However, the distributed collective nature of these motifs intrinsically limits the ability of Hopfield-Potts models in predicting contact maps, showing the necessity of developing models going beyond the Hopfield-Potts models discussed here.

The Three-Dimensional Structure of the Herbicide Binding Niche on the Reaction Center Polypeptides of Photosystem II

1987 ◽  
Vol 42 (6) ◽  
pp. 742-750 ◽  
Author(s):  
Achim Trebst
Keyword(s):  
Amino Acid ◽  
Photosystem Ii ◽  
Reaction Center ◽  
Three Dimensional ◽  
Chemical Compounds ◽  
Dimensional Structure ◽  
Bacterial Reaction Center ◽  
Protein Subunits ◽  
Herbicide Binding ◽  
Hydropathy Analysis

The folding through the membrane of the plastoquinone and herbicide binding protein subunits of photosystem II and the topology of the binding niche for plastoquinone and herbicides is described. The model is based on the homology in amino acid sequence and folding prediction from the hydropathy analysis of the D-1 and D-2 subunits of photosystem II to the reaction center polypeptides L and M of the bacterial reaction center. It incorporates the amino acid changes in the D-1 polypeptide in herbicide tolerant plants and those indicated by chemical tagging to be involved in Qв binding. It proposes homologous amino acids in the D-1/D-2 polypeptides to those indicated by the X-ray structure of the bacterial reaction center to be involved in Fe-, quinone- and reaction center chlorophyll-binding. The different chemical compounds known to interfere with Qв function are grouped into two families depending on their orientation in the Qв binding niche.

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