Enhancing a long-range salt bridge with intermediate aromatic and nonpolar amino acids

Smith, M.S.; Billings, W.M.; Whitby, Frank G.; Miller, McKenzie B.; Price, Joshua L.

doi:10.1039/c7ob01198a

Cited by 14 publications

(34 citation statements)

References 47 publications

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“…The obtained X-ray crystal structure of R288H apo (PDB ID: 7E2O) and WT apo (PDB ID: 2ZK0) 9) were compared (Figs. 3a-d, f) and showed that Arg288 and Glu295 formed a long-range salt bridge [13][14][15][16][17][18][19][20][21] in WT (Fig. 3b).…”

Section: Resultsmentioning

confidence: 92%

Structural Insights into the Loss-of-Function R288H Mutant of Human PPARγ

Egawa

Ogiso

Nishikata

et al. 2021

Biological & Pharmaceutical Bulletin

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Peroxisome proliferator-activated receptor gamma (PPARγ) is a nuclear receptor and the molecular target of thiazolidinedione-class antidiabetic drugs. It has been reported that the loss of function R288H mutation in the human PPARγ ligand-binding domain (LBD) may be associated with the onset of colon cancer. A previous in vitro study showed that this mutation dampens 15-deoxy-Δ 12,14 -prostaglandin J2 (15d-PGJ2, a natural PPARγ agonist)-dependent transcriptional activation; however, it is poorly understood why the function of the R288H mutant is impaired and what role this arginine (Arg) residue plays. In this study, we found that the apo-form of R288H PPARγ mutant displays several altered conformational arrangements of the amino acid side chains in LBD: 1) the loss of a salt bridge between Arg288 and Glu295 leads to increased helix 3 movement; 2) closer proximity of Gln286 and His449 via a hydrogen bond, and closer proximity of Cys285 and Phe363 via hydrophobic interaction, stabilize the helix 3-helix 11 interaction; and 3) there is steric hindrance between Cys285/Gln286/Ser289/His449 and the flexible ligands 15d-PGJ2, 6-oxotetracosahexaenoic acid (6-oxoTHA), and 17-oxodocosahexaenoic acid (17-oxoDHA). These results suggest why Arg288 plays an important role in ligand binding and why the R288H mutation is disadvantageous for flexible ligand binding.

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Section: Resultsmentioning

confidence: 92%

Structural Insights into the Loss-of-Function R288H Mutant of Human PPARγ

Egawa

Ogiso

Nishikata

et al. 2021

Biological & Pharmaceutical Bulletin

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“…Solid-Phase Synthesis: General probe synthesis procedures were adapted from those of Mason Smith based on his previous work in peptide synthesis (Smith, Billings et al 2017).…”

Section: Probe Synthesis and Purificationmentioning

confidence: 99%

“…The fiber orientation distribution within an undeformed ROI (i.e. region between a pair of consecutive photobleach stripes) of a fascicle and ROI strain were used to predict the fiber orientation distribution of respective deformed configuration of the ROI assuming affine deformation by using following relation (Smith, Billings et al 2017).…”

Section: Evaluation Of Collagen Fiber Deformation Behavior and Degradation Dependentmentioning

confidence: 99%

Heterogeneous strains in tissue collagen show that high strains locally suppress degradation by collagenase

Saini

Tiwari

Cho

et al. 2021

Preprint

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Collagen, the most abundant protein in mammals, contributes to the physical properties of different tissues during development, homeostasis, and disease. The adaptation of physical properties of tissues to mechanical stimuli is thus dependent on the control of tissue collagen levels by well-regulated synthesis and degradation of collagen. Importantly, how various molecular-level events within a tissue sustaining a range of mechanical strains contribute towards maintaining its collagen levels, remains unclear to date. Such molecular level processes in tissues are studied here in the case of isolated tendons consisting of collagen fibrils oriented along tissue loading-axis and beating embryonic hearts to gain understanding of mechanical load dependent tissue sculpting. Using a novel bioreactor design, starved mice tail tendon fascicles were used as a "cell-free" model and were subjected to heterogeneous and uniaxial deformation modes. Patterned photobleaching of fluorescent probes, a novel Aza-peptide or dye, on fascicles used to quantify tissue strains. Tissue microstructure was simultaneously imaged using second harmonic generation (SHG) signal to assess tissue collagen content while deformed fascicle samples were exposed to purified matrix metalloproteinase-1 (MMP-1) or bacterial collagenase (BC). A decrease in the degradation rate (relative to strain-free) was observed for physiological strain limits of tendon tissue (i.e. ~5-8%) while at higher strains (i.e. pathological) the degradation rate was independent of strain magnitude changes. Interestingly, the strain dependence of degradation rate was independent of cleavage-site specificity of the collagenase molecules and the mode of tendon tissue deformation. Although spatially different within a tissue sample, the values of strain, degradation rate and collagen fiber organization with time during degradation of each tendon fascicle region were highly correlated. Tendon regions dominated by collagen fibers inclined to fascicle-axis were observed to follow non-affine deformation. The dependence of the degradation rate on mechanical strain is due to sequestration of collagen cleavage sites within fibrils. Permeation, tissue mass density and mobility of fluorescent collagenase and dextran are strain-independent for fascicle strains up to ~5-8% while the degradation rate is positively correlated to unfolded triple-helical collagen content. Normal beating chick hearts subjected to ~5% peak strain in a spatiotemporal coordinate contractile wave were observed to maintain their collagen mass until the beating strain is suppressed by inhibition of myosin-II. Based on the presence of exogeneous MMP inhibitors, endogenous MMPs within the non-beating hearts degrade the collagens immediately (in ~30-60 mins). Both tissue systems under mechanical strains suggest degradative sculpting where mechanical strain-dependent collagen fibril architecture changes appear to play a key role in determining collagen lifetime within tissues.

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“…However, the formation of a salt bridge was suggested through the interaction of a positively charged amino acid with a negatively charged one, potentially contributing to protein conformational stability, especially when these two ionic groups are located adjacent to each other [22]. In addition, the aliphatic index of CGT-BS indicates a higher value and showed a close similitude to other selected CGTases proteins, hence indicating thermally stable CGTase proteins.…”

Section: Prediction Of Theoretical Physicochemical Properties Of β-Cyclodextrin Glycosyltransferase (Cgt-bs)mentioning

confidence: 99%

Combined Optimization of Codon Usage and Glycine Supplementation Enhances the Extracellular Production of a β-Cyclodextrin Glycosyltransferase from Bacillus sp. NR5 UPM in Escherichia coli

Nik-Pa

Sobri

Abd‐Aziz

et al. 2020

IJMS

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Two optimization strategies, codon usage modification and glycine supplementation, were adopted to improve the extracellular production of Bacillus sp. NR5 UPM β-cyclodextrin glycosyltransferase (CGT-BS) in recombinant Escherichia coli. Several rare codons were eliminated and replaced with the ones favored by E. coli cells, resulting in an increased codon adaptation index (CAI) from 0.67 to 0.78. The cultivation of the codon modified recombinant E. coli following optimization of glycine supplementation enhanced the secretion of β-CGTase activity up to 2.2-fold at 12 h of cultivation as compared to the control. β-CGTase secreted into the culture medium by the transformant reached 65.524 U/mL at post-induction temperature of 37 °C with addition of 1.2 mM glycine and induced at 2 h of cultivation. A 20.1-fold purity of the recombinant β-CGTase was obtained when purified through a combination of diafiltration and nickel-nitrilotriacetic acid (Ni-NTA) affinity chromatography. This combined strategy doubled the extracellular β-CGTase production when compared to the single approach, hence offering the potential of enhancing the expression of extracellular enzymes, particularly β-CGTase by the recombinant E. coli.

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Enhancing a long-range salt bridge with intermediate aromatic and nonpolar amino acids

Cited by 14 publications

References 47 publications

Structural Insights into the Loss-of-Function R288H Mutant of Human PPARγ

Structural Insights into the Loss-of-Function R288H Mutant of Human PPARγ

Heterogeneous strains in tissue collagen show that high strains locally suppress degradation by collagenase

Combined Optimization of Codon Usage and Glycine Supplementation Enhances the Extracellular Production of a β-Cyclodextrin Glycosyltransferase from Bacillus sp. NR5 UPM in Escherichia coli

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