Journal articles: '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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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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7

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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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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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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Goldstein, J. M., T. Kordula, J. L. Moon, J. A. Mayo, and J. Travis. "Characterization of an Extracellular Dipeptidase from Streptococcus gordonii FSS2." Infection and Immunity 73, no. 2 (February 2005): 1256–59. http://dx.doi.org/10.1128/iai.73.2.1256-1259.2005.

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ABSTRACT PepV, a dipeptidase found in culture fluids of Streptococcus gordonii FSS2, was purified and characterized, and its gene was cloned. PepV is a monomeric metalloenzyme of approximately 55 kDa that preferentially degrades hydrophobic dipeptides. The gene encodes a polypeptide of 467 amino acids, with a theoretical molecular mass of 51,114 Da and a calculated pI of 4.8. The S. gordonii PepV gene is homologous to the PepV gene family from Lactobacillus and Lactococcus spp.

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Afonso, R., A. Mendes, and L. Gales. "Hydrophobic dipeptide crystals: a promising Ag-free class of ultramicroporous materials showing argon/oxygen adsorption selectivity." Phys. Chem. Chem. Phys. 16, no. 36 (2014): 19386–93. http://dx.doi.org/10.1039/c4cp02085e.

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Wei, Chenyu, and Andrew Pohorille. "Fast bilayer-micelle fusion mediated by hydrophobic dipeptides." Biophysical Journal 120, no. 11 (June 2021): 2330–42. http://dx.doi.org/10.1016/j.bpj.2021.04.012.

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Otto, C., S. tom Dieck, and K. Bauer. "Dipeptide uptake by adenohypophysial folliculostellate cells." American Journal of Physiology-Cell Physiology 271, no. 1 (July 1, 1996): C210—C217. http://dx.doi.org/10.1152/ajpcell.1996.271.1.c210.

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Dipeptide uptake was studied in primary cultures from rat anterior pituitaries by use of radiolabeled carnosine and the fluorescent dipeptide derivative beta-Ala-Lys-N epsilon-AMCA (AMCA is 7-amino-4-methylcoumarin-3-acetic acid). Fluorescence microscopic studies revealed that the reporter peptide specifically accumulated in the S-100 positive folliculostellate cells that do not produce any known hormone. The dipeptide derivative was taken up in unmetabolized form by an energy-dependent saturable process with apparent kinetic constants as follows: Michaelis constant, 19 microM; maximum velocity, 5.5 nmol.mg protein-1.h-1. This high-affinity transporter was strongly affected by inhibitors of sodium/proton exchangers and thus appeared to be driven by a proton gradient. Competition studies revealed that the peptide transporter exhibits broad substrate specificity with a preference for hydrophobic dipeptides. In contrast to free amino acids and the pseudotetrapeptide amastatin, tripeptides were also accepted. Compounds without an alpha- and beta-amino group, such as captopril, thiorphan, and benzylpenicillin, did not affect uptake of the reporter peptide, although they were substrates of the well-characterized intestinal and renal dipeptide transporters.

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Görbitz, Carl Henrik. "Crystal structure ofL-leucyl-L-isoleucine 2,2,2-trifluoroethanol monosolvate." Acta Crystallographica Section E Crystallographic Communications 72, no. 5 (April 5, 2016): 635–38. http://dx.doi.org/10.1107/s2056989016005302.

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Hydrophobic dipeptides with either L-Leu or L-Phe constitute a rather heterogeneous group of crystal structures. Some form materials with large water-filled channels, but there is also a pronounced tendency to incorporate organic solvent molecules, which then act as acceptors for one of the three H atoms of the charged N-terminal amino group. L-Leu-L-Ile has uniquely been obtained as two distinct hydrates, but has so far failed to co-crystallize with a simple alcohol. The present structure of C12H24N2O3·CF3CH2OH, which crystallizes with two dipeptide and two solvent molecules in the asymmetric unit, demonstrates that when 2,2,2-trifluoroethanol is used as a solvent, its high capacity as a hydrogen-bond donor leads to formation of an alcohol solvate.

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Xu and Chung. "Quantitative Structure–Activity Relationship Study of Bitter Di-, Tri- and Tetrapeptides Using Integrated Descriptors." Molecules 24, no. 15 (August 5, 2019): 2846. http://dx.doi.org/10.3390/molecules24152846.

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New quantitative structure–activity relationship (QSAR) models for bitter peptides were built with integrated amino acid descriptors. Datasets contained 48 dipeptides, 52 tripeptides and 23 tetrapeptides with their reported bitter taste thresholds. Independent variables consisted of 14 amino acid descriptor sets. A bootstrapping soft shrinkage approach was utilized for variable selection. The importance of a variable was evaluated by both variable selecting frequency and standardized regression coefficient. Results indicated model qualities for di-, tri- and tetrapeptides with R2 and Q2 at 0.950 ± 0.002, 0.941 ± 0.001; 0.770 ± 0.006, 0.742 ± 0.004; and 0.972 ± 0.002, 0.956 ± 0.002, respectively. The hydrophobic C-terminal amino acid was the key determinant for bitterness in dipeptides, followed by the contribution of bulky hydrophobic N-terminal amino acids. For tripeptides, hydrophobicity of C-terminal amino acids and the electronic properties of the amino acids at the second position were important. For tetrapeptides, bulky hydrophobic amino acids at N-terminus, hydrophobicity and partial specific volume of amino acids at the second position, and the electronic properties of amino acids of the remaining two positions were critical. In summary, this study not only constructs reliable models for predicting the bitterness in different groups of peptides, but also facilitates better understanding of their structure-bitterness relationships and provides insights for their future studies.

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Görbitz, C. H. "Crystal structures of hydrophobic dipeptides as hosts for organic solvent molecules." Acta Crystallographica Section A Foundations of Crystallography 62, a1 (August 6, 2006): s73. http://dx.doi.org/10.1107/s0108767306098540.

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Murphy, Kenneth P., and Stanley J. Gill. "Thermodynamics of dissolution of solid cyclic dipeptides containing hydrophobic side groups." Journal of Chemical Thermodynamics 21, no. 9 (September 1989): 903–13. http://dx.doi.org/10.1016/0021-9614(89)90149-3.

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Henrik Görbitz, Carl. "Nanotubes from hydrophobic dipeptides: pore size regulation through side chain substitution." New J. Chem. 27, no. 12 (2003): 1789–93. http://dx.doi.org/10.1039/b305984g.

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Görbitz, C. H. "Hydrophobic dipeptides as building blocks for the construction of nanoporous organic materials." Acta Crystallographica Section A Foundations of Crystallography 63, a1 (August 22, 2007): s2—s3. http://dx.doi.org/10.1107/s0108767307099953.

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Krix, G., U. Eichhorn, H. D. Jakubke, and M. R. Kula. "Protease-catalyzed synthesis of new hydrophobic dipeptides containing non-proteinogenic amino acids." Enzyme and Microbial Technology 21, no. 4 (September 1997): 252–57. http://dx.doi.org/10.1016/s0141-0229(97)00037-9.

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Li, Tao, Michail Kalloudis, Andre Zamith Cardoso, Dave J. Adams, and Paul S. Clegg. "Drop-Casting Hydrogels at a Liquid Interface: The Case of Hydrophobic Dipeptides." Langmuir 30, no. 46 (June 6, 2014): 13854–60. http://dx.doi.org/10.1021/la501182t.

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23

Ootubo, Toshiro, Shunsaku Kimura, and Yukio Imanishi. "Interaction of Hydrophobic Cyclic Dipeptides and Acylbenzenes as Studied by Fluorescent Quenching." Bulletin of the Chemical Society of Japan 58, no. 10 (October 1985): 2870–74. http://dx.doi.org/10.1246/bcsj.58.2870.

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Hamley, Ian W., Ge Cheng, and Valeria Castelletto. "A Thermoresponsive Hydrogel Based on Telechelic PEG End-Capped with Hydrophobic Dipeptides." Macromolecular Bioscience 11, no. 8 (May 6, 2011): 1068–78. http://dx.doi.org/10.1002/mabi.201100022.

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Scarel, Erica, Giovanni Pierri, Petr Rozhin, Simone Adorinni, Maurizio Polentarutti, Consiglia Tedesco, and Silvia Marchesan. "Self-Assembly and Gelation Study of Dipeptide Isomers with Norvaline and Phenylalanine." Chemistry 4, no. 4 (November 2, 2022): 1417–28. http://dx.doi.org/10.3390/chemistry4040093.

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Dipeptides have emerged as attractive building blocks for supramolecular materials thanks to their low-cost, inherent biocompatibility, ease of preparation, and environmental friendliness as they do not persist in the environment. In particular, hydrophobic amino acids are ideal candidates for self-assembly in polar and green solvents, as a certain level of hydrophobicity is required to favor their aggregation and reduce the peptide solubility. In this work, we analyzed the ability to self-assemble and the gel of dipeptides based on the amino acids norvaline (Nva) and phenylalanine (Phe), studying all their combinations and not yielding to enantiomers, which display the same physicochemical properties, and hence the same self-assembly behavior in achiral environments as those studied herein. A single-crystal X-ray diffraction of all the compounds revealed fine details over their molecular packing and non-covalent interactions.

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Cantacuzene, Dani�le, Catherine Guerreiro, and Sandra Attal. "Influence of hydrophobic amino acid residues on the esterification of dipeptides by papain." Biotechnology Letters 11, no. 7 (July 1989): 493–98. http://dx.doi.org/10.1007/bf01026648.

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Sakamoto, Hiroshi, Yasuyuki Shimohigashi, Iori Maeda, Takeru Nose, Kin-ichi Nakashima, Ichiro Nakamura, Tomoshisa Ogawa, Motonori Ohno, and Keiichi Kawano. "Chymotrypsin inhibitory conformation of dipeptides constructed by side chain-side chain hydrophobic interactions." Journal of Molecular Recognition 6, no. 2 (June 1993): 95–100. http://dx.doi.org/10.1002/jmr.300060207.

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Görbitz, C. H., and P. H. Backe. "Structures of L-valyl-L-glutamine and L-glutamyl-L-valine." Acta Crystallographica Section B Structural Science 52, no. 6 (December 1, 1996): 999–1006. http://dx.doi.org/10.1107/s0108768196006817.

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L-Val-L-Gln crystallizes in the orthorhombic space group P21212 with a = 16.419 (3), b = 15.309 (3) and c = 4.708 (1) Å. The final wR(F o 2) is 0.100 for 2044 independent reflections, R(Fo ) = 0.050 for 1475 reflections with I > 2.0σ(I). L-Glu-L-Val crystallizes in the monoclinic space group P21 with a = 6.487 (2), b = 5.505 (2), c = 16.741 (4) Å and β = 97.22 (2)°. The final wR(F F o 2) is 0.111 for 1920 independent reflections, R(Fo ) = 0.047 for 1576 reflections with I > 2.0σ(I). Molecular geometries are normal, except for a unique eclipsed orientation of the charged amino group of L-Glu-L-Val. Dipeptides with a N-terminal hydrophobic residue and C-terminal hydrophilic residue are shown to have crystal packing patterns fundamentally different from those of dipeptides with the same types of residues in reversed order. Accordingly, the structure of L-Val-L-Glu [Eggleston (1984). Acta Cryst. C40, 1250 –1252] is rather similar to L-Val-L-Gln, but different from its retroanalogue L-Glu-L-Val. Nevertheless, the pairing of hydrogen-bond donors and acceptors is the same for L-Val-L-Glu and L-Glu-L-Val, indicating very distinct hydrogen-bonding preferences. This is the first demonstration of such a coincidence among dipeptide structures. The differences between L-Val-L-Glu and L-Val-L-Gln structures stem from modifications of the molecular geometry and cell parameters due to the formation of an additional hydrogen bond from the extra donor in the L-Gln side chain.

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Babizhayev, Mark A. "Designation of imidazole-containing dipeptides as pharmacological chaperones." Human & Experimental Toxicology 30, no. 7 (July 23, 2010): 736–61. http://dx.doi.org/10.1177/0960327110377526.

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We review the dichotomous regulatory roles of natural imidazole-containing peptidomimetics (N-acetylcarnosine [NAC], carcinine, non-hydrolized carnosine) in maintaining skin homeostasis that determines whether keratinocytes survive or undergo apoptosis in response to various insults and in the development of skin diseases. General strategies addressing common ground techniques to improve absorption of usually active chaperone proteins or their dipeptide inducer (usually poorly absorbed) compounds include encapsulation into hydrophobic carriers, combination with penetration enhancers, active electrical transport or chemical modification to increase hydrophobicity. A growing evidence is presented that demonstrates the ability of NAC (lubricant eye drops) or carcinine to act as pharmacological chaperones, or being synergistically coupled in patented formulations with another imidazole-containing peptidomimetic (such as, Leucyl-histidylhydrazide), to decrease oxidative stress and ameliorate oxidative and excessive glycation stress-related eye disease phenotypes, suggesting that the field of chaperone therapy might hold novel treatments for age-related cataracts, glaucoma, age-related macular degeneration (AMD), and ocular complications of diabetes (OCD). Current efforts are being directed towards exploring therapeutic approaches of pharmacological targeting and human drug delivery for chaperone molecules based on innovative patented strategies.

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Bombelli, Cecilia, Stefano Borocci, Oscar Cruciani, Giovanna Mancini, Donato Monti, Anna Laura Segre, Alessandro Sorrenti, and Mariano Venanzi. "Chiral recognition of dipeptides in bio-membrane models: the role of amphiphile hydrophobic chains." Tetrahedron: Asymmetry 19, no. 1 (January 2008): 124–30. http://dx.doi.org/10.1016/j.tetasy.2007.11.035.

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Krishnan, G. Rajesh, Yuan Yuan, Ayesha Arzumand, and Debanjan Sarkar. "Gelation characteristics and applications of poly(ethylene glycol) end capped with hydrophobic biodegradable dipeptides." Journal of Polymer Science Part A: Polymer Chemistry 52, no. 14 (April 22, 2014): 1917–28. http://dx.doi.org/10.1002/pola.27198.

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He, Ronghai, Haile Ma, Weirui Zhao, Wenjuan Qu, Jiewen Zhao, Lin Luo, and Wenxue Zhu. "Modeling the QSAR of ACE-Inhibitory Peptides with ANN and Its Applied Illustration." International Journal of Peptides 2012 (June 9, 2012): 1–9. http://dx.doi.org/10.1155/2012/620609.

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A quantitative structure-activity relationship (QSAR) model of angiotensin-converting enzyme- (ACE-) inhibitory peptides was built with an artificial neural network (ANN) approach based on structural or activity data of 58 dipeptides (including peptide activity, hydrophilic amino acids content, three-dimensional shape, size, and electrical parameters), the overall correlation coefficient of the predicted versus actual data points is , and the model was applied in ACE-inhibitory peptides preparation from defatted wheat germ protein (DWGP). According to the QSAR model, the C-terminal of the peptide was found to have principal importance on ACE-inhibitory activity, that is, if the C-terminal is hydrophobic amino acid, the peptide's ACE-inhibitory activity will be high, and proteins which contain abundant hydrophobic amino acids are suitable to produce ACE-inhibitory peptides. According to the model, DWGP is a good protein material to produce ACE-inhibitory peptides because it contains 42.84% of hydrophobic amino acids, and structural information analysis from the QSAR model showed that proteases of Alcalase and Neutrase were suitable candidates for ACE-inhibitory peptides preparation from DWGP. Considering higher DH and similar ACE-inhibitory activity of hydrolysate compared with Neutrase, Alcalase was finally selected through experimental study.

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Soldatov, Dmitriy, Abdolreza Yazdani, Julia Crewson, Travis Fillion, Aaron Smith, and Melissa Ignacio. "Porous peptide frameworks generated by stacking non-self-complementary β-sheets." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C562. http://dx.doi.org/10.1107/s2053273314094376.

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"One of major approaches in the design of cavity space in the solids utilizes non-self-complementary molecules[1]. The irregular shape of the molecules and/or specific directionality of potential H-bonds prevent close packing of the molecules and yields various architectures hosting a second component, from inclusion compounds and co-crystals to complex non-crystalline patterns in biology. The strategy of non-self-complementary molecules has been extended in our studies to 2D supramolecular polymers based on short peptides[2]. The formation of the peptide layer with a desired overall geometry is controlled by strong, charge-assisted H-bonds (arrows in the Figure) in a β-sheet-like network as well as the segregation of hydrophobic amino acid residues into the interlayer space. The H-bonds add stability to the whole architecture while the hydrophobic groups keep the stacking layers at a distance that generates a cavity space available to a second component (encircled ""G"" in the Figure). A wide range of inclusions and co-crystals have been prepared in our group based on a series of dipeptides and higher peptide oligomers. For example, the incorporation of various organic solvents and bioactive molecules have been demonstrated for leucyl-alanine and similar dipeptides: alcohols, amides, phenols, pyridines, polyols, vitamins, scents and flavors. The crystal structure studies reveal a surprisingly persistent structural motif that can be used for engineering of crystalline materials with a specific property. We believe this type of peptide matrix may be utilized in the solid state organic synthesis [3] as reactive molecules of the second component can be oriented in a predictable way with respect to each other. "

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Görbitz, Carl Henrik. "β Turns, water cage formation and hydrogen bonding in the structures of L-valyl-L-phenylalanine." Acta Crystallographica Section B Structural Science 58, no. 3 (May 29, 2002): 512–18. http://dx.doi.org/10.1107/s010876810200277x.

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L-Valyl-L-phenylalanine has been crystallized as an orthorhombic dihydrate (1) in the shape of needles and as a monoclinic trihydrate (2) with Z = 16 (P21, Z′ = 8) in the shape of thin plates. Peptide molecules in these two structures occur in three basic conformations, termed c 1, c 2A and c 2B. c 2B has not been observed previously for dipeptides. Together with c 1 it forms a model pair for Type I and Type II β-turns in protein structures. The crystal packing of (2) is remarkable in that some of the L-Val side chains are exposed to the solvent region of the crystal rather than being located in a hydrophobic layer. The crystal packing thus offers a unique and detailed view of hydrogen-bond cage formation around the hydrophobic groups by the 24 cocrystallized water molecules. The eight —NH_3^+...−OOC— contacts in the structure are unusually short and the minimum N...O distance of 2.649 (5) Å represents a new extreme limit for this type of hydrogen bond in peptide structures.

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Hudecz, Ferenc, and Mária Szekerke. "Synthesis of new branched polypeptides with poly(lysine)back bone." Collection of Czechoslovak Chemical Communications 50, no. 1 (1985): 103–13. http://dx.doi.org/10.1135/cccc19850103.

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New analogues of branched polypeptides were synthesised for a further, more detailed study of the influence of the side chain terminating amino acids, particularly the hydrophobic character, configuration and the number of these amino acids, on the conformation and biological properties of the polymers. The following amino acids were coupled to poly(L-Lys-(DL-Alam)) in suitably protected and activated forms to study the above mentioned aspects: L-Nlc, L-Ile, L-Val, L-Phe, D-Phe, D-Leu, D-Tyr, D-His, L-Glu, D-Glu, L-Lys, D-Lys and additionally the L-Glu-L-Glu, D-Glu-D-Glu, L-Lys-L-Lys and D-Lys-D-Lys dipeptides. The deprotected and purified end products were freezedried and characterized by various methods.

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Savijoki, Kirsi, and Airi Palva. "Purification and Molecular Characterization of a Tripeptidase (PepT) from Lactobacillus helveticus." Applied and Environmental Microbiology 66, no. 2 (February 1, 2000): 794–800. http://dx.doi.org/10.1128/aem.66.2.794-800.2000.

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ABSTRACT A tripeptidase (PepT) from a thermophilic dairy starter strain ofLactobacillus helveticus was purified by four chromatographic steps. PepT appeared to be a trimeric metallopeptidase with a molecular mass of 150 kDa. PepT exhibited maximum activity against hydrophobic tripeptides, with the highest activity for Met-Gly-Gly (Km , 2.6 mM;V max, 80.2 μmol · min−1 · μg−1). Some of the hydrophobic dipeptides were slowly hydrolyzed, distinguishing theLactobacillus PepT from its counterpart in mesophilicLactococcus lactis. No activity against tetrapeptides or amino acid p-nitroanilide derivatives was observed. ThepepT gene and its flanking regions were isolated by PCR and sequenced by cyclic sequencing. The sequence analyses revealed open reading frames (ORFs) 816 bp (ORF1) and 1,239 bp (ORF2) long. ORF2 encoded a 47-kDa PepT protein which exhibited 53% identity with the PepT from L. lactis. The mRNA analyses indicated thatpepT conforms a novel operon structure with an ORF1 located upstream. Several putative −35/−10 regions preceded the operon, but only one transcription start site located downstream of the first putative −10 region was identified. An inverted repeat structure with ΔG of −64.8 kJ/mol was found downstream of the PepT-encoding region.

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Sanz, Yolanda, and Fidel Toldrá. "Purification and Characterization of an Arginine Aminopeptidase from Lactobacillus sakei." Applied and Environmental Microbiology 68, no. 4 (April 2002): 1980–87. http://dx.doi.org/10.1128/aem.68.4.1980-1987.2002.

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ABSTRACT An arginine aminopeptidase (EC 3.4.11.6) that exclusively hydrolyzes basic amino acids from the amino (N) termini of peptide substrates has been purified from Lactobacillus sakei. The purification procedure consisted of ammonium sulfate fractionation and three chromatographic steps, which included hydrophobic interaction, gel filtration, and anion-exchange chromatography. This procedure resulted in a recovery rate of 4.2% and a 500-fold increase in specific activity. The aminopeptidase appeared to be a trimeric enzyme with a molecular mass of 180 kDa. The activity was optimal at pH 5.0 and 37°C. The enzyme was inhibited by sulfhydryl group reagents and several divalent cations (Cu2+, Hg2+, and Zn2+) but was activated by reducing agents, metal-chelating agents, and sodium chloride. The enzyme showed a preference for arginine at the N termini of aminoacyl derivatives and peptides. The Km values for Arg-7-amido-4-methylcoumarin (AMC) and Lys-AMC were 15.9 and 26.0 μM, respectively. The nature of the amino acid residue at the C terminus of dipeptides has an effect on hydrolysis rates. The activity was maximal toward dipeptides with Arg, Lys, or Ala as the C-terminal residue. The properties of the purified enzyme, its potential function in the release of arginine, and its further metabolism are discussed because, as a whole, it could constitute a survival mechanism for L. sakei in the meat environment.

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Mowatt, M. R., and C. E. Clayton. "Developmental regulation of a novel repetitive protein of Trypanosoma brucei." Molecular and Cellular Biology 7, no. 8 (August 1987): 2838–44. http://dx.doi.org/10.1128/mcb.7.8.2838-2844.1987.

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Trypanosoma brucei undergoes many morphological and biochemical changes during transformation from the bloodstream trypomastigote to the insect procyclic trypomastigote form. We cloned and determined the complete nucleotide sequence of a developmentally regulated cDNA. The corresponding mRNA was abundant in in vitro-cultivated procyclics but absent in bloodstream forms. The trypanosome genome contains eight genes homologous to this cDNA, arranged as four unlinked pairs of tandem repeats. The longest open reading frame of the cDNA predicts a protein of 15 kilodaltons, the central portion of which consists of 29 tandem glutamate-proline dipeptides. The repetitive region is preceded by an amino-terminal signal sequence and followed by a hydrophobic domain that could serve as a membrane anchor; the mRNA was found on membrane-bound polyribosomes. These results suggest that the protein is membrane associated.

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39

Mowatt, M. R., and C. E. Clayton. "Developmental regulation of a novel repetitive protein of Trypanosoma brucei." Molecular and Cellular Biology 7, no. 8 (August 1987): 2838–44. http://dx.doi.org/10.1128/mcb.7.8.2838.

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Trypanosoma brucei undergoes many morphological and biochemical changes during transformation from the bloodstream trypomastigote to the insect procyclic trypomastigote form. We cloned and determined the complete nucleotide sequence of a developmentally regulated cDNA. The corresponding mRNA was abundant in in vitro-cultivated procyclics but absent in bloodstream forms. The trypanosome genome contains eight genes homologous to this cDNA, arranged as four unlinked pairs of tandem repeats. The longest open reading frame of the cDNA predicts a protein of 15 kilodaltons, the central portion of which consists of 29 tandem glutamate-proline dipeptides. The repetitive region is preceded by an amino-terminal signal sequence and followed by a hydrophobic domain that could serve as a membrane anchor; the mRNA was found on membrane-bound polyribosomes. These results suggest that the protein is membrane associated.

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Kęska, Paulina, Joanna Stadnik, Olga Bąk, and Piotr Borowski. "Meat Proteins as Dipeptidyl Peptidase IV Inhibitors and Glucose Uptake Stimulating Peptides for the Management of a Type 2 Diabetes Mellitus In Silico Study." Nutrients 11, no. 10 (October 21, 2019): 2537. http://dx.doi.org/10.3390/nu11102537.

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Diabetes mellitus is a non-communicable disease entity currently constituting one of the most significant health problems. The development of effective therapeutic strategies for the prevention and/or treatment of diabetes mellitus based on the selection of methods to restore and maintain blood glucose homeostasis is still in progress. Among the different courses of action, inhibition of dipeptidyl peptidase IV (DPP-IV) can improve blood glucose control in diabetic patients. Pharmacological therapy offering synthetic drugs is commonly used. In addition to medication, dietary intervention may be effective in combating metabolic disturbances caused by diabetes mellitus. Food proteins as a source of biologically active sequences are a potential source of anti-diabetic peptides (DPP-IV inhibitors and glucose uptake stimulating peptides). This study showed that in silico pork meat proteins digested with gastrointestinal enzymes are a potential source of bioactive peptides with a high potential to control blood glucose levels in patients with type 2 diabetes mellitus. Analysis revealed that the sequences released during in silico digestion were small dipeptides (with an average weight of 270.07 g mol−1), and most were poorly soluble in water. The selected electron properties of the peptides with the highest bioactivity index (i.e., GF, MW, MF, PF, PW) were described using the DFT method. The contribution of hydrophobic amino acids, in particular Phe and Trp, in forming the anti-diabetic properties of peptides released from pork meat was emphasized.

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Zhang, Shitao, Shuai Lv, Xueqi Fu, Lu Han, Weiwei Han, and Wannan Li. "Molecular Dynamics Simulations Study of the Interactions between Human Dipeptidyl-Peptidase III and Two Substrates." Molecules 26, no. 21 (October 27, 2021): 6492. http://dx.doi.org/10.3390/molecules26216492.

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Human dipeptidyl-peptidase III (hDPP III) is capable of specifically cleaving dipeptides from the N-terminal of small peptides with biological activity such as angiotensin II (Ang II, DRVYIHPF), and participates in blood pressure regulation, pain modulation, and the development of cancers in human biological activities. In this study, 500 ns molecular dynamics simulations were performed on free-hDPP III (PDB code: 5E33), hDPP III-Ang II (PDB code: 5E2Q), and hDPP III-IVYPW (PDB code: 5E3C) to explore how these two peptides affect the catalytic efficiency of enzymes in terms of the binding mode and the conformational changes. Our results indicate that in the case of the hDPP III-Ang II complex, subsite S1 became small and hydrophobic, which might be propitious for the nucleophile to attack the substrate. The structures of the most stable conformations of the three systems revealed that Arg421-Lys423 could form an α-helix with the presence of Ang II, but only part of the α-helix was produced in hDPP III-IVYPW. As the hinge structure in hDPP III, the conformational changes that took place in the Arg421-Lys423 residue could lead to the changes in the shape and space of the catalytic subsites, which might allow water to function as a nucleophile to attack the substrate. Our results may provide new clues to enable the design of new inhibitors for hDPP III in the future.

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Adasme Carreno, Francisco, Julio Caballero, and Joel Ireta. "Theoretical Study of the Intrinsic Conformational Preferences and Microsolvation Effect on the Self-Assembly of Hydrophobic L-Dipeptides." Biophysical Journal 120, no. 3 (February 2021): 293a. http://dx.doi.org/10.1016/j.bpj.2020.11.1878.

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43

Guo, Jian, Naoto Hirasaki, Yuji Miyata, Kazunari Tanaka, Takashi Tanaka, Xiao Wu, Yusuke Tahara, Kiyoshi Toko, and Toshiro Matsui. "Evaluating the Reduced Hydrophobic Taste Sensor Response of Dipeptides by Theasinensin A by Using NMR and Quantum Mechanical Analyses." PLOS ONE 11, no. 6 (June 16, 2016): e0157315. http://dx.doi.org/10.1371/journal.pone.0157315.

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44

Guan, Shanshan, Xu Han, Zhan Li, Xifei Xu, Yongran Cui, Zhiwen Chen, Shuming Zhang, et al. "Exploration of the Interactions between Maltase–Glucoamylase and Its Potential Peptide Inhibitors by Molecular Dynamics Simulation." Catalysts 12, no. 5 (May 7, 2022): 522. http://dx.doi.org/10.3390/catal12050522.

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Diabetes mellitus, a chronic metabolic disorder, represents a serious threat to human health. The gut enzyme maltase–glucoamylase (MGAM) has attracted considerable attention as a potential therapeutic target for the treatment of type 2 diabetes. Thus, developing novel inhibitors of MGAM holds the promise of improving clinical management. The dipeptides, Thr-Trp (TW) and Trp-Ala (WA), are known inhibitors of MGAM; however, studies on how they interact with MGAM are lacking. The work presented here explored these interactions by utilizing molecular docking and molecular dynamics simulations. Results indicate that the active center of the MGAM could easily accommodate the flexible peptides. Interactions involving hydrogen bonds, cation-π, and hydrophobic interactions are predicted between TW/WA and residues including Tyr1251, Trp1355, Asp1420, Met1421, Glu1423, and Arg1510 within MGAM. The electrostatic energy was recognized as playing a dominant role in both TW-MGAM and WA-MGAM systems. The binding locations of TW/WA are close to the possible acid-base catalytic residue Asp1526 and might be the reason for MGAM inhibition. These findings provide a theoretical structural model for the development of future inhibitors.

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Fang, Gang, Wil N. Konings, and Bert Poolman. "Kinetics and Substrate Specificity of Membrane-Reconstituted Peptide Transporter DtpT ofLactococcus lactis." Journal of Bacteriology 182, no. 9 (May 1, 2000): 2530–35. http://dx.doi.org/10.1128/jb.182.9.2530-2535.2000.

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ABSTRACT The peptide transport protein DtpT of Lactococcus lactis was purified and reconstituted into detergent-destabilized liposomes. The kinetics and substrate specificity of the transporter in the proteoliposomal system were determined, using Pro-[14C]Ala as a reporter peptide in the presence of various peptides or peptide mimetics. The DtpT protein appears to be specific for di- and tripeptides, with the highest affinities for peptides with at least one hydrophobic residue. The effect of the hydrophobicity, size, or charge of the amino acid was different for the amino- and carboxyl-terminal positions of dipeptides. Free amino acids, ω-amino fatty acid compounds, or peptides with more than three amino acid residues do not interact with DtpT. For high-affinity interaction with DtpT, the peptides need to have free amino and carboxyl termini, amino acids in the l configuration, andtrans-peptide bonds. Comparison of the specificity of DtpT with that of the eukaryotic homologues PepT1 and PepT2 shows that the bacterial transporter is more restrictive in its substrate recognition.

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Eaholtz, Galen, Anita Colvin, Daniele Leonard, Charles Taylor, and William A. Catterall. "Block of Brain Sodium Channels by Peptide Mimetics of the Isoleucine, Phenylalanine, and Methionine (IFM) Motif from the Inactivation Gate." Journal of General Physiology 113, no. 2 (February 1, 1999): 279–94. http://dx.doi.org/10.1085/jgp.113.2.279.

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Inactivation of sodium channels is thought to be mediated by an inactivation gate formed by the intracellular loop connecting domains III and IV. A hydrophobic motif containing the amino acid sequence isoleucine, phenylalanine, and methionine (IFM) is required for the inactivation process. Peptides containing the IFM motif, when applied to the cytoplasmic side of these channels, produce two types of block: fast block, which resembles the inactivation process, and slow, use-dependent block stimulated by strong depolarizing pulses. Fast block by the peptide ac-KIFMK-NH2, measured on sodium channels whose inactivation was slowed by the α-scorpion toxin from Leiurus quinquestriatus (LqTx), was reversed with a time constant of 0.9 ms upon repolarization. In contrast, control and LqTx-modified sodium channels were slower to recover from use-dependent block. For fast block, linear peptides of three to six amino acid residues containing the IFM motif and two positive charges were more effective than peptides with one positive charge, whereas uncharged IFM peptides were ineffective. Substitution of the IFM residues in the peptide ac-KIFMK-NH2 with smaller, less hydrophobic residues prevented fast block. The positively charged tripeptide IFM-NH2 did not cause appreciable fast block, but the divalent cation IFM-NH(CH2)2NH2 was as effective as the pentapeptide ac-KIFMK-NH2. The constrained peptide cyclic KIFMK containing two positive charges did not cause fast block. These results indicate that the position of the positive charges is unimportant, but flexibility or conformation of the IFM-containing peptide is important to allow fast block. Slow, use-dependent block was observed with IFM-containing peptides of three to six residues having one or two positive charges, but not with dipeptides or phenylalanine-amide. In contrast to its lack of fast block, cyclic KIFMK was an effective use-dependent blocker. Substitutions of amino acid residues in the tripeptide IFM-NH2 showed that large hydrophobic residues are preferred in all three positions for slow, use-dependent block. However, substitution of the large hydrophobic residue diphenylalanine or the constrained residues phenylglycine or tetrahydroisoquinoline for phe decreased potency, suggesting that this phe residue must be able to enter a restricted hydrophobic pocket during the binding of IFM peptides. Together, the results on fast block and slow, use-dependent block indicate that IFM peptides form two distinct complexes of different stability and structural specificity with receptor site(s) on the sodium channel. It is proposed that fast block represents binding of these peptides to the inactivation gate receptor, while slow, use-dependent block represents deeper binding of the IFM peptides in the pore.

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Onorato, Robert M., Alfred P. Yoon, James T. Lin, and Gabor A. Somorjai. "Adsorption of Amino Acids and Dipeptides to the Hydrophobic Polystyrene Interface Studied by SFG and QCM: The Special Case of Phenylalanine." Journal of Physical Chemistry C 116, no. 18 (May 2, 2012): 9947–54. http://dx.doi.org/10.1021/jp210879p.

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48

Wilson, Karl A., Mary Russell, John F. Quackenbush, and Anna L. Tan-Wilson. "Characterization of carboxypeptidase I of mung bean seeds." Seed Science Research 5, no. 4 (December 1995): 209–18. http://dx.doi.org/10.1017/s0960258500002877.

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AbstractThere is a carboxypeptidase in mung bean seeds that is localized in the protein bodies, the same vacuoles in which seed storage proteins are sequestered. This carboxypeptidase, called carboxypeptidase I (or Cpase I) has been purified by a series of ion-exchange and gel filtration columns. The pure enzyme consists of a single polypeptide chain with a MW of 41700 by SDS-PAGE or 42000 by size-exclusion HPLC. It has a pl of 4.36 and is a serine carboxypeptidase as shown by its inactivation by phenylmethylsulfonyl fluoride, and its resistance to other proteolytic inhibitory reagents. A survey of its activity with Cbz-dipeptides shows preference for C-terminal amino acids that are large, hydrophobic residues, and a small aliphatic amino acid such as alanine, but not glycine, at the penultimate amino acid residue. Cpase I can convert a trypsin inhibitor of the mung bean to its proteolytic intermediate lacking four amino acid residues at its C-terminus. This proteolytic intermediate is detected in the mung bean cotyledons during early growth. Levels of both the activity and immunological cross-reacting forms of this enzyme start high and decrease during early growth.

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Bode, Manuela, Michael W. Woellhaf, Maria Bohnert, Martin van der Laan, Frederik Sommer, Martin Jung, Richard Zimmermann, Michael Schroda, and Johannes M. Herrmann. "Redox-regulated dynamic interplay between Cox19 and the copper-binding protein Cox11 in the intermembrane space of mitochondria facilitates biogenesis of cytochrome c oxidase." Molecular Biology of the Cell 26, no. 13 (July 2015): 2385–401. http://dx.doi.org/10.1091/mbc.e14-11-1526.

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Members of the twin Cx9C protein family constitute the largest group of proteins in the intermembrane space (IMS) of mitochondria. Despite their conserved nature and their essential role in the biogenesis of the respiratory chain, the molecular function of twin Cx9C proteins is largely unknown. We performed a SILAC-based quantitative proteomic analysis to identify interaction partners of the conserved twin Cx9C protein Cox19. We found that Cox19 interacts in a dynamic manner with Cox11, a copper transfer protein that facilitates metalation of the Cu(B) center of subunit 1 of cytochrome c oxidase. The interaction with Cox11 is critical for the stable accumulation of Cox19 in mitochondria. Cox19 consists of a helical hairpin structure that forms a hydrophobic surface characterized by two highly conserved tyrosine-leucine dipeptides. These residues are essential for Cox19 function and its specific binding to a cysteine-containing sequence in Cox11. Our observations suggest that an oxidative modification of this cysteine residue of Cox11 stimulates Cox19 binding, pointing to a redox-regulated interplay of Cox19 and Cox11 that is critical for copper transfer in the IMS and thus for biogenesis of cytochrome c oxidase.

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Li, Congcong, Kaifeng Liu, Siao Chen, Lu Han, and Weiwei Han. "Gaussian Accelerated Molecular Dynamics Simulations Investigation on the Mechanism of Angiotensin-Converting Enzyme (ACE) C-Domain Inhibition by Dipeptides." Foods 11, no. 3 (January 25, 2022): 327. http://dx.doi.org/10.3390/foods11030327.

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Angiotensin-converting enzyme (ACE)-inhibitory peptides extracted from food proteins can lower blood pressure by inhibiting ACE activity. A recent study showed that the inhibitory activity of IY (Ile-Tyr, a dipeptide derived from soybean protein) against ACE was much higher than that of LL (Leu-Leu), although they had similar hydrophobic and predicted activity values. It was difficult to reveal the deep molecular mechanism underlying this phenomenon by traditional experimental methods. The Apo and two complex systems (i.e., ACE–LL and ACE–IY) were therefore subjected to 1 μs long Gaussian accelerated molecular dynamics (GaMD) simulations. The results showed that the binding of IY can cause obvious contraction of the active site of ACE, mainly manifested by a significant lateral shift of α13, α14, and α15. In addition, hinge 2 and hinge 3 were more stable in the ACE–IY system, while these phenomena were not present in the ACE–LL system. Moreover, the α10 of the IY-bound ACE kept an inward state during the simulation progress, which facilitated the ACE to remain closed. However, for the LL-bound ACE, the α10 switched between two outward states. To sum up, our study provides detailed insights into inhibitor-induced conformational changes in ACE that may help in the design of specific inhibitors targeting ACE for the treatment of hypertension.

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Journal articles on the topic 'Hydrophobic dipeptides'

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