Target Binding to S100B Reduces Dynamic Properties and Increases Ca2+-Binding Affinity for Wild Type and EF-Hand Mutant Proteins

: Vitamin-D deficiency is a global concern. Gene mutations in the vitamin D receptor’s (VDR) ligand binding domain (LBD) variously alter the ligand binding affinity, heterodimerization with retinoid X receptor (RXR) and inhibit coactivator interactions. These LBD mutations may result in partial or total hormone unresponsiveness. A plethora of evidence report that selective long chain polyunsaturated fatty acids (PUFAs) including eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA) and arachidonic acid (AA) bind to the ligand-binding domain of VDR and lead to transcriptional activation. We therefore hypothesize that selective PUFAs would modulate the dynamics and kinetics of VDRs, irrespective bioactive of vitamin-D binding. The spatial arrangements of the selected PUFAs in VDR active site were examined by in-silico docking studies. The docking results revealed that PUFAs have fatty acid structure-specific binding affinity towards VDR. The calculated EPA, DHA & AA binding energies (Cdocker energy) were lesser compared to vitamin-D in wild type of VDR (PDB id: 2ZLC). Of note, the DHA has higher binding interactions to the mutated VDR (PDB id: 3VT7) when compared to the standard Vitamin-D. Molecular dynamic simulation was utilized to confirm the stability of potential compound binding of DHA with mutated VDR complex. These findings suggest the unique roles of PUFAs in VDR activation and may offer alternate strategy to circumvent vitamin-D deficiency.

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Modulating Uranium Binding Affinity in Engineered Calmodulin EF-Hand Peptides: Effect of Phosphorylation

PLoS ONE ◽

10.1371/journal.pone.0041922 ◽

2012 ◽

Vol 7 (8) ◽

pp. e41922 ◽

Cited By ~ 42

Author(s):

Romain Pardoux ◽

Sandrine Sauge-Merle ◽

David Lemaire ◽

Pascale Delangle ◽

Luc Guilloreau ◽

...

Keyword(s):

Binding Affinity ◽

Ef Hand

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Investigation of the Stability of Yeast rad52 Mutant Proteins Uncovers Post-translational and Transcriptional Regulation of Rad52p

Genetics ◽

10.1093/genetics/163.1.91 ◽

2003 ◽

Vol 163 (1) ◽

pp. 91-101 ◽

Cited By ~ 1

Author(s):

Erin N Asleson ◽

Dennis M Livingston

Keyword(s):

Half Life ◽

Translational Regulation ◽

Cellular Level ◽

Missense Mutations ◽

Wild Type ◽

Mutant Proteins ◽

Gal1 Promoter ◽

Rad52 Protein ◽

The Stability ◽

Mutant Forms

Abstract We investigated the stability of the Saccharomyces cerevisiae Rad52 protein to learn how a cell controls its quantity and longevity. We measured the cellular levels of wild-type and mutant forms of Rad52p when expressed from the RAD52 promoter and the half-lives of the various forms of Rad52p when expressed from the GAL1 promoter. The wild-type protein has a half-life of 15 min. rad52 mutations variably affect the cellular levels of the protein products, and these levels correlate with the measured half-lives. While missense mutations in the N terminus of the protein drastically reduce the cellular levels of the mutant proteins, two mutations—one a deletion of amino acids 210-327 and the other a missense mutation of residue 235—increase the cellular level and half-life more than twofold. These results suggest that Rad52p is subject to post-translational regulation. Proteasomal mutations have no effect on Rad52p half-life but increase the amount of RAD52 message. In contrast to Rad52p, the half-life of Rad51p is >2 hr, and RAD51 expression is unaffected by proteasomal mutations. These differences between Rad52p and Rad51p suggest differential regulation of two proteins that interact in recombinational repair.

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Imbalance between Expression of FOXC2 and Its lncRNA in Lymphedema-Distichiasis Caused by Frameshift Mutations

Genes ◽

10.3390/genes12050650 ◽

2021 ◽

Vol 12 (5) ◽

pp. 650

Author(s):

Sara Missaglia ◽

Daniela Tavian ◽

Sandro Michelini ◽

Paolo Enrico Maltese ◽

Andrea Bonanomi ◽

...

Keyword(s):

Mrna Stability ◽

Healthy Subjects ◽

Lymphatic System ◽

System Development ◽

Bioinformatic Analysis ◽

Wild Type ◽

Mutant Proteins ◽

Frameshift Mutations ◽

Forkhead Box ◽

Frameshift Mutant

Forkhead-box C2 (FOXC2) is a transcription factor involved in lymphatic system development. FOXC2 mutations cause Lymphedema-distichiasis syndrome (LD). Recently, a natural antisense was identified, called lncRNA FOXC2-AS1, which increases FOXC2 mRNA stability. No studies have evaluated FOXC2 and FOXC2-AS1 blood expression in LD and healthy subjects. Here, we show that FOXC2 and FOXC-AS1 expression levels were similar in both controls and patients, and a significantly higher amount of both RNAs was observed in females. A positive correlation between FOXC2 and FOXC2-AS1 expression was found in both controls and patients, excluding those with frameshift mutations. In these patients, the FOXC2-AS1/FOXC2 ratio was about 1:1, while it was higher in controls and patients carrying other types of mutations. The overexpression or silencing of FOXC2-AS1 determined a significant increase or reduction in FOXC2 wild-type and frameshift mutant proteins, respectively. Moreover, confocal and bioinformatic analysis revealed that these variations caused the formation of nuclear proteins aggregates also involving DNA. In conclusion, patients with frameshift mutations presented lower values of the FOXC2-AS1/FOXC2 ratio, due to a decrease in FOXC2-AS1 expression. The imbalance between FOXC2 mRNA and its lncRNA could represent a molecular mechanism to reduce the amount of FOXC2 misfolded proteins, protecting cells from damage.

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Expression and purification of his-tagged rat peroxisomal acyl-CoA oxidase I wild-type and E421 mutant proteins

Protein Expression and Purification ◽

10.1016/j.pep.2004.08.013 ◽

2004 ◽

Vol 38 (1) ◽

pp. 153-160 ◽

Cited By ~ 23

Author(s):

Jia Zeng ◽

Ding Li

Keyword(s):

Wild Type ◽

Expression And Purification ◽

Mutant Proteins ◽

Acyl Coa Oxidase

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Solution structures of the trihelix DNA-binding domains of the wild-type and a phosphomimetic mutant of Arabidopsis GT-1: Mechanism for an increase in DNA-binding affinity through phosphorylation

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.22827 ◽

2010 ◽

Vol 78 (14) ◽

pp. 3033-3047 ◽

Cited By ~ 21

Author(s):

Takashi Nagata ◽

Emi Niyada ◽

Natsuki Fujimoto ◽

Yuuya Nagasaki ◽

Kazuaki Noto ◽

...

Keyword(s):

Dna Binding ◽

Binding Affinity ◽

Wild Type ◽

Solution Structures ◽

Dna Binding Domains ◽

Binding Domains ◽

Dna Binding Affinity

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Requirement of PKR Dimerization Mediated by Specific Hydrophobic Residues for Its Activation by Double-Stranded RNA and Its Antigrowth Effects in Yeast

Molecular and Cellular Biology ◽

10.1128/mcb.18.12.7009 ◽

1998 ◽

Vol 18 (12) ◽

pp. 7009-7019 ◽

Cited By ~ 40

Author(s):

Rekha C. Patel ◽

Ganes C. Sen

Keyword(s):

Helical Structure ◽

Wild Type ◽

Dimerization Domain ◽

Double Stranded Rna ◽

Mutant Proteins ◽

Hydrophobic Residues ◽

Dsrna Binding ◽

Dependent Protein ◽

Substitution Mutations

ABSTRACT The roles of protein dimerization and double-stranded RNA (dsRNA) binding in the biochemical and cellular activities of PKR, the dsRNA-dependent protein kinase, were investigated. We have previously shown that both properties of the protein are mediated by the same domain. Here we show that dimerization is mediated by hydrophobic residues present on one side of an amphipathic α-helical structure within this domain. Appropriate substitution mutations of residues on that side produced mutants with increased or decreased dimerization activities. Using these mutants, we demonstrated that dimerization is not essential for dsRNA binding. However, enhancing dimerization artificially, by providing an extraneous dimerization domain, increased dsRNA binding of both wild-type and mutant proteins. In vitro, the dimerization-defective mutants could not be activated by dsRNA but were activated normally by heparin. In Saccharomyces cerevisiae, unlike wild-type PKR, these mutants could not inhibit cell growth and the dsRNA-binding domain of the dimerization-defective mutants could not prevent the antigrowth effect of wild-type PKR. These results demonstrate the biological importance of the dimerization properties of PKR.

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Helicase Motif Ia Is Involved in Single-Strand DNA-Binding and Helicase Activities of the Herpes Simplex Virus Type 1 Origin-Binding Protein, UL9

Journal of Virology ◽

10.1128/jvi.77.4.2477-2488.2003 ◽

2003 ◽

Vol 77 (4) ◽

pp. 2477-2488 ◽

Cited By ~ 16

Author(s):

Boriana Marintcheva ◽

Sandra K. Weller

Keyword(s):

Herpes Simplex ◽

Atpase Activity ◽

Structural Information ◽

Origin Of Replication ◽

Wild Type ◽

Mutant Proteins ◽

Ssdna Binding ◽

Simplex Virus ◽

Hsv 1

ABSTRACT UL9 is a multifunctional protein essential for herpes simplex virus type 1 (HSV-1) replication in vivo. UL9 is a member of the superfamily II helicases and exhibits helicase and origin-binding activities. It is thought that UL9 binds the origin of replication and unwinds it in the presence of ATP and the HSV-1 single-stranded DNA (ssDNA)-binding protein. We have previously characterized the biochemical properties of mutants in all helicase motifs except for motif Ia (B. Marintcheva and S. Weller, J. Biol. Chem. 276:6605-6615, 2001). Structural information for other superfamily I and II helicases indicates that motif Ia is involved in ssDNA binding. By analogy, we hypothesized that UL9 motif Ia is important for the ssDNA-binding function of the protein. On the basis of sequence conservation between several UL9 homologs within the Herpesviridae family and distant homology with helicases whose structures have been solved, we designed specific mutations in motif Ia and analyzed them genetically and biochemically. Mutant proteins with residues predicted to be involved in ssDNA binding (R112A and R113A/F115A) exhibited wild-type levels of intrinsic ATPase activity and moderate to severe defects in ssDNA-stimulated ATPase activity and ssDNA binding. The S110T mutation targets a residue not predicted to contact ssDNA directly. The mutant protein with this mutation exhibited wild-type levels of intrinsic ATPase activity and near wild-type levels of ssDNA-stimulated ATPase activity and ssDNA binding. All mutant proteins lack helicase activity but were able to dimerize and bind the HSV-1 origin of replication as well as wild-type UL9. Our results indicate that residues from motif Ia contribute to the ssDNA-binding and helicase activities of UL9 and are essential for viral growth. This work represents the successful application of an approach based on a combination of bioinformatics and structural information from related proteins to deduce valuable information about a protein of interest.

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Analysis of Genomes Changes in Pseudomonas Chlororaphis Subsp. Aurantiaca Strains Producing Phenazines

10.21203/rs.3.rs-289228/v1 ◽

2021 ◽

Author(s):

Anastasia I. Liaudanskaya ◽

Natalia P. Maximova ◽

Katsiaryna G. Verameyenka

Keyword(s):

Mutant Strain ◽

Phenylalanine Hydroxylase ◽

Response Regulator ◽

Trna Genes ◽

Type I ◽

Pseudomonas Chlororaphis ◽

Wild Type ◽

Mutant Proteins ◽

Domain Structures ◽

Genome Annotations

Abstract Genomes of three strains – phenazine producers – Pseudomonas chlororaphis subsp. aurantiaca (B-162 (wild-type), mutant strain B-162/255 and its derivatives B-162/17) were sequenced and compared. All genome annotations revealed 6347 CDS, 5 rRNA clusters (5S, 16S, 23S) and 59 tRNA genes. Comparison analysis of wild-type strain and B-162/255 mutant strain genomes allowed revealing 32 mutations. 19 new mutations were detected upon comparison of genomes strains B-162/255 and B-162/17. Further bioinformatics analysis allowed predicting mutant proteins` functions and secondary structures of five gene products, mutations in which might potentially have influence on phenazine synthesis and secretion in Pseudomonas bacteria. These genes are phenylalanine hydroxylase transcriptional activator PhhR, type I secretion system ATPase, transcriptional regulator MvaT, GacA response regulator and histidine kinase. Amino acid substitutions were located in domain structures of corresponding proteins.

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