Relevant bibliographies by topics / Hydrophobic dipeptides

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Academic literature on the topic 'Hydrophobic dipeptides'

Author: Grafiati
Published: 9 March 2023
Last updated: 10 March 2023

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Journal articles on the topic "Hydrophobic dipeptides"

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Zainol, Mohamad K. M., Robert J. C. Linforth, Donald J. Winzor, and David J. Scott. "Thermodynamics of semi-specific ligand recognition: the binding of dipeptides to the E.coli dipeptide binding protein DppA." European Biophysics Journal 50, no. 8 (October 5, 2021): 1103–10. http://dx.doi.org/10.1007/s00249-021-01572-y.

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AbstractThis investigation of the temperature dependence of DppA interactions with a subset of three dipeptides (AA. AF and FA) by isothermal titration calorimetry has revealed the negative heat capacity ($$\Delta {C}_{p}^{o}$$ Δ C p o ) that is a characteristic of hydrophobic interactions. The observation of enthalpy–entropy compensation is interpreted in terms of the increased structuring of water molecules trapped in a hydrophobic environment, the enthalpic energy gain from which is automatically countered by the entropy decrease associated with consequent loss of water structure flexibility. Specificity for dipeptides stems from appropriate spacing of designated DppA aspartate and arginine residues for electrostatic interaction with the terminal amino and carboxyl groups of a dipeptide, after which the binding pocket closes to become completely isolated from the aqueous environment. Any differences in chemical reactivity of the dipeptide sidechains are thereby modulated by their occurrence in a hydrophobic environment where changes in the structural state of entrapped water molecules give rise to the phenomenon of enthalpy–entropy compensation. The consequent minimization of differences in the value of ΔG0 for all DppA–dipeptide interactions thus provides thermodynamic insight into the biological role of DppA as a transporter of all dipeptides across the periplasmic membrane.
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Li, Chun-Yang, Xiu-Lan Chen, Qi-Long Qin, Peng Wang, Wei-Xin Zhang, Bin-Bin Xie, Hai-Nan Su, Xi-Ying Zhang, Bai-Cheng Zhou, and Yu-Zhong Zhang. "Structural Insights into the Multispecific Recognition of Dipeptides of Deep-Sea Gram-Negative Bacterium Pseudoalteromonas sp. Strain SM9913." Journal of Bacteriology 197, no. 6 (January 20, 2015): 1125–34. http://dx.doi.org/10.1128/jb.02600-14.

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ABSTRACTPeptide uptake is important for nutrition supply for marine bacteria. It is also an important step in marine nitrogen cycling. However, how marine bacteria absorb peptides is still not fully understood. DppA is the periplasmic dipeptide binding protein of dipeptide permease (Dpp; an important peptide transporter in bacteria) and exclusively controls the substrate specificity of Dpp. Here, the substrate binding specificity of deep-seaPseudoalteromonassp. strain SM9913 DppA (PsDppA) was analyzed for 25 different dipeptides with various properties by using isothermal titration calorimetry measurements.PsDppA showed binding affinities for 8 dipeptides. To explain the multispecific substrate recognition mechanism ofPsDppA, we solved the crystal structures of unligandedPsDppA and ofPsDppA in complex with 4 different types of dipeptides (Ala-Phe, Met-Leu, Gly-Glu, and Val-Thr).PsDppA alternates between an “open” and a “closed” form during substrate binding. Structural analyses of the 4PsDppA-substrate complexes combined with mutational assays indicate thatPsDppA binds to different substrates through a precise mechanism: dipeptides are bound mainly by the interactions between their backbones andPsDppA, in particular by anchoring their N and C termini through ion-pair interactions; hydrophobic interactions are important in binding hydrophobic dipeptides; and Lys457 is necessary for the binding of dipeptides with a C-terminal glutamic acid or glutamine. Additionally, sequence alignment suggests that the substrate recognition mechanism ofPsDppA may be common in Gram-negative bacteria. All together, our results provide structural insights into the multispecific substrate recognition mechanism of marine Gram-negative bacterial DppA, which provides a better understanding of the mechanisms of marine bacterial peptide uptake.IMPORTANCEPeptide uptake plays a significant role in nutrition supply for marine bacteria. It is also an important step in marine nitrogen cycling. However, how marine bacteria recognize and absorb peptides is still unclear. This study analyzed the substrate binding specificity of deep-seaPseudoalteromonassp. strain SM9913 DppA (PsDppA; the dipeptide-binding protein of dipeptide permease) and solved the crystal structures of unligandedPsDppA andPsDppA in complex with 4 different types of dipeptides. The multispecific recognition mechanism ofPsDppA for dipeptides is explained based on structural and mutational analyses. We also find that the substrate-binding mechanism ofPsDppA may be common in Gram-negative bacteria. This study sheds light on marine Gram-negative bacterial peptide uptake and marine nitrogen cycling.
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Görbitz, Carl Henrik. "Hydrophobic dipeptides: the final piece in the puzzle." Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials 74, no. 3 (May 24, 2018): 311–18. http://dx.doi.org/10.1107/s2052520618007151.

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The crystal structure of L-valyl-L-leucine acetonitrile solvate presented here adds to 24 previously reported structures of dipeptides constructed from the five nonpolar amino acids L-alanine, L-valine, L-isoleucine, L-leucine and L-phenylalanine. It thus constitutes the final piece in the 5 × 5 puzzle of hydrophobic dipeptide structures. This opportunity is taken to review the crystal packing arrangements and hydrogen-bonding preferences of a rather unique group of substances, with updated information on the various hydrogen-bonding patterns and the associated peptide conformations.
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Vikram, Amit, Vanessa M. Ante, X. Renee Bina, Qin Zhu, Xinyu Liu, and James E. Bina. "Cyclo(valine–valine) inhibits Vibrio cholerae virulence gene expression." Microbiology 160, no. 6 (June 1, 2014): 1054–62. http://dx.doi.org/10.1099/mic.0.077297-0.

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Vibrio cholerae has been shown to produce a cyclic dipeptide, cyclo(phenylalanine–proline) (cFP), that functions to repress virulence factor production. The objective of this study was to determine if heterologous cyclic dipeptides could repress V. cholerae virulence factor production. To that end, three synthetic cyclic dipeptides that differed in their side chains from cFP were assayed for virulence inhibitory activity in V. cholerae. The results revealed that cyclo(valine–valine) (cVV) inhibited virulence factor production by a ToxR-dependent process that resulted in the repression of the virulence regulator aphA. cVV-dependent repression of aphA was found to be independent of known aphA regulatory genes. The results demonstrated that V. cholerae was able to respond to exogenous cyclic dipeptides and implicated the hydrophobic amino acid side chains on both arms of the cyclo dipeptide scaffold as structural requirements for inhibitory activity. The results further suggest that cyclic dipeptides have potential as therapeutics for cholera treatment.
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Thiele, D. L., and P. E. Lipsky. "The action of leucyl-leucine methyl ester on cytotoxic lymphocytes requires uptake by a novel dipeptide-specific facilitated transport system and dipeptidyl peptidase I-mediated conversion to membranolytic products." Journal of Experimental Medicine 172, no. 1 (July 1, 1990): 183–94. http://dx.doi.org/10.1084/jem.172.1.183.

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The mechanism of toxicity for cytolytic lymphocytes of Leu-Leu-OMe and related dipeptide derivatives was examined. Selective inhibition of dipeptidyl peptidase I (DPPI), a lysosomal thiol protease highly enriched in cytotoxic lymphocytes, prevented all natural killer (NK) toxic effects of such agents. However, many DPPI substrates were found to possess no NK toxic properties. For some such agents, this lack of NK toxicity appeared to be related to the lack of uptake by lymphocytes. In this regard, Leu-Leu-OMe was found to be incorporated by lymphocytes and monocytes via a saturable facilitated transport mechanism with characteristics distinct from previously characterized mammalian dipeptide transport processes. This novel transport process was found to be specific for dipeptides composed of selective L-stereoisomer amino acids and enhanced by hydrophobic ester or amide additions to the COOH terminus of dipeptides. Maximal rates of Leu-Leu-OMe uptake by T8 and NK cell-enriched peripheral blood lymphocytes (PBL) were four- to sixfold higher than for T4-enriched PBL or PBL depleted of Leu-Leu-OMe-sensitive cytotoxic lymphocytes. All dipeptide amides or esters with NK toxic properties were found to act as competitive inhibitors of [3H]Leu-Leu-OMe uptake by PBL. However, some NK nontoxic DPPI substrates were found to be comparable with Leu-Leu-OMe in avidity for this transport process. Such agents were noted to possess one or more hydrophilic amino acid side chains and were found not to mediate red blood cell lysis when subjected to the acyl transferase activity of DPPI. Thus, uptake by a dipeptide-specific facilitated transport mechanism and conversion by DPPI to hydrophobic polymerization products with membranolytic properties were found to be common features of NK toxic dipeptide derivatives. The presence of a previously unreported dipeptide transport mechanism within blood leukocytes and the selective enrichment of the granule enzyme, DPPI, within cytotoxic effector cells of lymphoid or myeloid lineage appear to afford a unique mechanism for the targeting of immunotherapeutic reagents composed of simple dipeptide esters or amides.
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6

Görbitz, Carl Henrik. "Nanotube Formation by Hydrophobic Dipeptides." Chemistry - A European Journal 7, no. 23 (December 3, 2001): 5153–59. http://dx.doi.org/10.1002/1521-3765(20011203)7:23<5153::aid-chem5153>3.0.co;2-n.

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Kovačević, Monika, Mojca Čakić Semenčić, Ivan Kodrin, Sunčica Roca, Jana Perica, Jasna Mrvčić, Damir Stanzer, et al. "Biological Evaluation and Conformational Preferences of Ferrocene Dipeptides with Hydrophobic Amino Acids." Inorganics 11, no. 1 (January 3, 2023): 29. http://dx.doi.org/10.3390/inorganics11010029.

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Despite the large number of peptidomimetics with incorporated heteroannularly functionalized ferrocenes, few studies have investigated their bioactivity. Here, we report the biological evaluation and conformational analysis of enantiomeric dipeptides derived from 1′-aminoferrocene-1-carboxylic acid (Fca) and hydrophobic amino acids (AA = Val, Leu, Phe). The conformational properties of Y-AA-Fca-OMe (Y = Ac, Boc) were elucidated by experimental (IR, NMR, CD, and X-ray) and theoretical (DFT) methods. The prepared dipeptides were screened for their antimicrobial activity against selected Gram-positive and Gram-negative bacteria, lactic acid bacteria and yeasts, while their antioxidant activity was tested by DPPH and FRAP methods. Of all compounds tested, dipeptide D-2a showed the best antibacterial properties against S. aureus, B. subtilis, and P. aeruginosa at a concentration of 2 mM. The time–kill curves showed that antibacterial activity was concentration- and time-dependent. Chirality (D-) and a more polar-protecting group (Ac) were found to affect the biological activity, both antimicrobial and antioxidant. All investigated peptides are considered to be highly hydrophobic and chemically stable in both acidic and buffer media. Dipeptides D-1a–3a, which showed biological activity, were subjected to the determination of proteolytic activity, revealing very good resistance to proteolysis in the presence of chymotrypsin.
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8

Görbitz, Carl Henrik, and Vitthal N. Yadav. "N-(L-2-Aminopentanoyl)-L-phenylalanine dihydrate, a hydrophobic dipeptide with a nonproteinogenic residue." Acta Crystallographica Section C Crystal Structure Communications 69, no. 9 (August 13, 2013): 1067–69. http://dx.doi.org/10.1107/s0108270113021914.

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The title dipeptide, better known as L-norvalyl-L-phenylalanine {systematic name: (S)-2-[(S)-2-aminopentanamido]-3-phenylpropanoic acid dihydrate}, C14H20N2O3·2H2O, has a nonproteinogenic N-terminal residue. In the solid state, it takes on a molecular conformation typical for one of the three classes of nanoporous dipeptides, but like two related compounds with a hydrophobic N-terminal residue and a C-terminal L-phenylalanine, it fails to form channels or pores. Instead, the crystal structure is divided into distinct hydrophobic and hydrophilic layers, the latter encompassing cocrystallized water molecules connecting the charged N- and C-terminal groups.
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9

Görbitz, Carl Henrik. "Microporous Organic Materials from Hydrophobic Dipeptides." Chemistry - A European Journal 13, no. 4 (January 22, 2007): 1022–31. http://dx.doi.org/10.1002/chem.200601427.

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10

Itoh, Ryota, Yusuke Kurihara, Michinobu Yoshimura, and Kenji Hiromatsu. "Bortezomib Eliminates Persistent Chlamydia trachomatis Infection through Rapid and Specific Host Cell Apoptosis." International Journal of Molecular Sciences 23, no. 13 (July 4, 2022): 7434. http://dx.doi.org/10.3390/ijms23137434.

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Chlamydia trachomatis, a parasitic intracellular bacterium, is a major human pathogen that causes millions of trachoma, sexually transmitted infections, and pneumonia cases worldwide. Previously, peptidomimetic inhibitors consisting of a hydrophobic dipeptide derivative exhibited significant inhibitory effects against chlamydial growth. Based on this finding, this study showed that both bortezomib (BTZ) and ixazomib (IXA), anticancer drugs characterized by proteasome inhibitors, have intensive inhibitory activity against Chlamydia. Both BTZ and IXA consisted of hydrophobic dipeptide derivatives and strongly restricted the growth of Chlamydia (BTZ, IC50 = 24 nM). In contrast, no growth inhibitory effect was observed for other nonintracellular parasitic bacteria, such as Escherichia coli. BTZ and IXA appeared to inhibit chlamydial growth bacteriostatically via electron microscopy. Surprisingly, Chlamydia-infected cells that induced a persistent infection state were selectively eliminated by BTZ treatment, whereas uninfected cells survived. These results strongly suggested the potential of boron compounds based on hydrophobic dipeptides for treating chlamydial infections, including persistent infections, which may be useful for future therapeutic use in chlamydial infectious diseases.
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Dissertations / Theses on the topic "Hydrophobic dipeptides"

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DISTEFANO, GAETANO. "Nanoporous dipeptide crystals as selective gas sorbents and polymerization nanovessels." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2012. http://hdl.handle.net/10281/29103.

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Hydrophobic dipeptide crystals recently emerged as novel “organic zeolites” featuring tailorable pore size. In fact, seven out of nine pairwise combinations of L-isoleucine, L-valine and L-alanine amino acids crystallize according to the same charge-assisted hydrogen bond pattern, generating a family of microporous materials with right-handed 1D channels, having diameters in the sub-nanometer domain (<6Å), aliphatic environment and different degrees of helicity. The relationship between pore size and material properties was investigated with respect to gas separation, exploiting the affinity of carbon dioxide for the hydrophobic nanochannels of L-alanyl-L-valine (AV), L-isoleucyl-L-valine (IV) and L-valyl-L-isoleucine (VI). Reversible CO2 capture from an equimolar mixture of CO2 and methane, at room temperature and 1 atmosphere, was demonstrated with increasing purification performance with decrease in pore size. Dipeptide were also used as nanovessels in radical polymerizations with the aim of controlling otherwise non-specific reactions. Diene monomers (trans-1,3-pentadiene and isoprene) only yield linear 1,4-trans polymer in accordance with 1-dimensional pore geometry, while poly(acrylonitrile) (PAN) could be obtained as a stereoregular isotactic product by acrylonitrile polymerization in AV dipeptide. Finally, taking advantage of the dipeptide lability and unique thermal properties of poly(acrylonitrile), AV-PAN nanocomposites were used as a scaffold to obtain carbon replicas of the starting nanocomposite crystals (carbon micro-fibrils) showing anisotropic arrangement of the graphite domains.
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Afonso, Rui Vieira. "Experimental results and theoretical investigation of adsorption of gases in crystalline hydrophobic dipeptides." Doctoral thesis, 2016. https://repositorio-aberto.up.pt/handle/10216/83817.

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Afonso, Rui Vieira. "Experimental results and theoretical investigation of adsorption of gases in crystalline hydrophobic dipeptides." Tese, 2016. https://repositorio-aberto.up.pt/handle/10216/83817.

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