Journal articles: 'Folded Peptides'

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Venkatraman, Janani, Sasalu C. Shankaramma, and Padmanabhan Balaram. "Design of Folded Peptides†." Chemical Reviews 101, no. 10 (October 2001): 3131–52. http://dx.doi.org/10.1021/cr000053z.

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Chatterjee, Sunanda, Rituparna Sinha Roy, and P. Balaram. "Expanding the polypeptide backbone: hydrogen-bonded conformations in hybrid polypeptides containing the higher homologues of α-amino acids." Journal of The Royal Society Interface 4, no. 15 (January 23, 2007): 587–606. http://dx.doi.org/10.1098/rsif.2006.0203.

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Half a century has passed since the hydrogen-bonded secondary structures of polypeptides and proteins were first recognized. An extraordinary wealth of conformational information is now available on peptides and proteins, which are formed of α-amino acid residues. More recently, the discovery of well-folded structures in oligopeptides containing β-amino acids has focused a great deal of current interest on the conformational properties of peptides constructed from higher homologues (ω) of α-amino acids. This review examines the nature of intramolecularly hydrogen-bonded conformations of hybrid peptides formed by amino acid residues, with a varying number of backbone atoms. The β-turn, a ubiquitous structural feature formed by two residue (αα) segments in proteins and peptides, is stabilized by a 10-atom (C 10 ) intramolecular 4→1 hydrogen bond. Hybrid turns may be classified by comparison with their αα counterparts. The available crystallographic information on hydrogen-bonded hybrid turns is surveyed in this review. Several recent examples demonstrate that individual ω-amino acid residues and hybrid dipeptide segments may be incorporated into the regular structures of α-peptides. Examples of both peptide helices and hairpins are presented. The present review explores the relationships between folded conformations in hybrid sequences and their counterparts in all α-residue sequences. The use of stereochemically constrained ω-residues promises to expand the range of peptide design strategies to include ω-amino acids. This approach is exemplified by well-folded structures like the C 12 (αγ) and C 14 (γγ) helices formed in short peptides containing multiply substituted γ-residues. The achiral γ-residue gabapentin is a readily accessible building block in the design of peptides containing γ-amino acids. The construction of globular polypeptide structures using diverse hybrid sequences appears to be a realistic possibility.

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Venkatraman, Janani, Sasalu C. Shankaramma, and Padmanabhan Balaram. "ChemInform Abstract: Design of Folded Peptides." ChemInform 32, no. 52 (May 23, 2010): no. http://dx.doi.org/10.1002/chin.200152270.

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Yuan, Xiushuang, Linhai Jiang, Weike Chen, Bo Song, Wei Chen, Xiaobing Zuo, Xiankai Sun, et al. "Self-assembly of chimeric peptides toward molecularly defined hexamers with controlled multivalent ligand presentation." Chemical Communications 56, no. 52 (2020): 7128–31. http://dx.doi.org/10.1039/d0cc02066d.

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In this work, we report the self-assembly of chimeric peptides in which two distinctly folded domains can be organized into a finite peptide hexamer with precise control over multivalent ligand presentation and enhanced tumor cell targeting.

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Saini, Sunil Kumar, Katja Ostermeir, Venkat Raman Ramnarayan, Martin Zacharias, and Sebastian Springer. "Dipeptides enhance folding and peptide binding of “empty” MHC class I molecules (P5002)." Journal of Immunology 190, no. 1_Supplement (May 1, 2013): 41.2. http://dx.doi.org/10.4049/jimmunol.190.supp.41.2.

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Abstract MHC (Major Histocompatibility Complex) class I molecules play a central role in the mammalian antiviral immune response by presenting the viral proteome at the cell surface for recognition by cytotoxic T lymphocytes. The folding of recombinant MHC class I molecules from denatured bacterial inclusion bodies and their assembly with the light chain beta-2 microglobulin largely depend on specific high-affinity peptides of usually eight or nine amino acids. To find the minimum peptide requirement for folding and stabilization of class I molecules, we have investigated the influence of dipeptides on the folding and peptide binding of recombinant HLA-A*02:01 (A2) and H-2Kb (Kb). In the presence of the dipeptide Gly-Leu (GL), both A2 and Kb folded well, even without a high-affinity peptide present, as measured by a tryptophan fluorescence assay. When folded in the presence of GL, they also bound much faster to their respective specific high-affinity peptides as when folded without GL. Kinetic analysis by fluorescence anisotropy revealed that the presence of GL enhances the on-rate of peptide binding to empty A2 and Kb by six to eight fold. Molecular dynamics simulation indicates that the dipeptide GL interacts with the C terminus of the peptide binding groove. In conclusion, our data demonstrate that the dipeptide GL improves the folding of A2 and Kb and induces a peptide-receptive conformation for enhanced peptide binding.

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Arai, Kenta, and Michio Iwaoka. "Flexible Folding: Disulfide-Containing Peptides and Proteins Choose the Pathway Depending on the Environments." Molecules 26, no. 1 (January 2, 2021): 195. http://dx.doi.org/10.3390/molecules26010195.

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In the last few decades, development of novel experimental techniques, such as new types of disulfide (SS)-forming reagents and genetic and chemical technologies for synthesizing designed artificial proteins, is opening a new realm of the oxidative folding study where peptides and proteins can be folded under physiologically more relevant conditions. In this review, after a brief overview of the historical and physicochemical background of oxidative protein folding study, recently revealed folding pathways of several representative peptides and proteins are summarized, including those having two, three, or four SS bonds in the native state, as well as those with odd Cys residues or consisting of two peptide chains. Comparison of the updated pathways with those reported in the early years has revealed the flexible nature of the protein folding pathways. The significantly different pathways characterized for hen-egg white lysozyme and bovine milk α-lactalbumin, which belong to the same protein superfamily, suggest that the information of protein folding pathways, not only the native folded structure, is encoded in the amino acid sequence. The application of the flexible pathways of peptides and proteins to the engineering of folded three-dimensional structures is an interesting and important issue in the new realm of the current oxidative protein folding study.

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Huang, Sheng-Yu, Tin-Yu Wei, Bing-Shin Liu, Min-Han Lin, Sheng-Kuo Chiang, Sung-Fang Chen, and Wang-Chou Sung. "Monitoring the Disulfide Bonds of Folding Isomers of Synthetic CTX A3 Polypeptide Using MS-Based Technology." Toxins 11, no. 1 (January 17, 2019): 52. http://dx.doi.org/10.3390/toxins11010052.

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Native disulfide formation is crucial to the process of disulfide-rich protein folding in vitro. As such, analysis of the disulfide bonds can be used to track the process of the folding reaction; however, the diverse structural isomers interfere with characterization due to the non-native disulfide linkages. Previously, a mass spectrometry (MS) based platform coupled with peptide demethylation and an automatic disulfide bond searching engine demonstrated the potential to screen disulfide-linked peptides for the unambiguous assignment of paired cysteine residues of toxin components in cobra venom. The developed MS-based platform was evaluated to analyze the disulfide bonds of structural isomers during the folding reaction of synthetic cardiotoxin A3 polypeptide (syn-CTX A3), an important medical component in cobra venom. Through application of this work flow, a total of 13 disulfide-linked peptides were repeatedly identified across the folding reaction, and two of them were found to contain cysteine pairings, like those found in native CTX A3. Quantitative analysis of these disulfide-linked peptides showed the occurrence of a progressive disulfide rearrangement that generates a native disulfide bond pattern on syn-CTX A3 folded protein. The formation of these syn-CTX A3 folded protein reaches a steady level in the late stage of the folding reaction. Biophysical and cell-based assays showed that the collected syn-CTX A3 folded protein have a β-sheet secondary structure and cytotoxic activity similar to that of native CTX A3. In addition, the immunization of the syn-CTX A3 folded proteins could induce neutralization antibodies against the cytotoxic activity of native CTX A3. In contrast, these structure activities were poorly observed in the other folded isomers with non-native disulfide bonds. The study highlights the ability of the developed MS platform to assay isomers with heterogeneous disulfide bonds, providing insight into the folding mechanism of the bioactive protein generation.

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Calabrese, Antonio N., Lauren A. Speechley, and Tara L. Pukala. "Characterisation of Calmodulin Structural Transitions by Ion Mobility Mass Spectrometry." Australian Journal of Chemistry 65, no. 5 (2012): 504. http://dx.doi.org/10.1071/ch12047.

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This study demonstrates the ability of travelling wave ion mobility-mass spectrometry to measure collision cross-sections of ions in the negative mode, using a calibration based approach. Here, negative mode ion mobility-mass spectrometry was utilised to understand structural transitions of calmodulin upon Ca2+ binding and complexation with model peptides melittin and the plasma membrane Ca2+ pump C20W peptide. Coexisting calmodulin conformers were distinguished on the basis of their mass and cross-section, and identified as relatively folded and unfolded populations, with good agreement in collision cross-section to known calmodulin geometries. Titration of calcium tartrate to physiologically relevant Ca2+ levels provided evidence for intermediately metalated species during the transition from apo- to holo-calmodulin, with collision cross-section measurements indicating that higher Ca2+ occupancy is correlated with more compact structures. The binding of two representative peptides which exemplify canonical compact (melittin) and extended (C20W) peptide-calmodulin binding models has also been interrogated by ion mobility mass spectrometry. Peptide binding to calmodulin involves intermediates with metalation states from 1–4 Ca2+, which demonstrate relatively collapsed structures, suggesting neither the existence of holo-calmodulin or a pre-folded calmodulin conformation is a prerequisite for binding target peptides or proteins. The biological importance of the different metal unsaturated calmodulin complexes, if any, is yet to be understood.

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9

Maurer, Carlo, Sascha Panahandeh, Anna-Carina Jungkamp, Michael Moser, and Matthias Müller. "TatB Functions as an Oligomeric Binding Site for Folded Tat Precursor Proteins." Molecular Biology of the Cell 21, no. 23 (December 2010): 4151–61. http://dx.doi.org/10.1091/mbc.e10-07-0585.

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Twin-arginine-containing signal sequences mediate the transmembrane transport of folded proteins. The cognate twin-arginine translocation (Tat) machinery of Escherichia coli consists of the membrane proteins TatA, TatB, and TatC. Whereas Tat signal peptides are recognized by TatB and TatC, little is known about molecular contacts of the mature, folded part of Tat precursor proteins. We have placed a photo-cross-linker into Tat substrates at sites predicted to be either surface-exposed or hidden in the core of the folded proteins. On targeting of these variants to the Tat machinery of membrane vesicles, all surface-exposed sites were found in close proximity to TatB. Correspondingly, incorporation of the cross-linker into TatB revealed multiple precursor-binding sites in the predicted transmembrane and amphipathic helices of TatB. Large adducts indicative of TatB oligomers contacting one precursor molecule were also obtained. Cross-linking of Tat substrates to TatB required an intact twin-arginine signal peptide and disappeared upon transmembrane translocation. Our collective data are consistent with TatB forming an oligomeric binding site that transiently accommodates folded Tat precursors.

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Kraft, Jennifer R., Russell E. Vance, Jan Pohl, Amy M. Martin, David H. Raulet, and Peter E. Jensen. "Analysis of Qa-1bPeptide Binding Specificity and the Capacity of Cd94/Nkg2a to Discriminate between Qa-1–Peptide Complexes." Journal of Experimental Medicine 192, no. 5 (August 28, 2000): 613–24. http://dx.doi.org/10.1084/jem.192.5.613.

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The major histocompatibility complex class Ib protein, Qa-1b, serves as a ligand for murine CD94/NKG2A natural killer (NK) cell inhibitory receptors. The Qa-1b peptide-binding site is predominantly occupied by a single nonameric peptide, Qa-1 determinant modifier (Qdm), derived from the leader sequence of H-2D and L molecules. Five anchor residues were identified in this study by measuring the peptide-binding affinities of substituted Qdm peptides in experiments with purified recombinant Qa-1b. A candidate peptide-binding motif was determined by sequence analysis of peptides eluted from Qa-1 that had been folded in the presence of random peptide libraries or pools of Qdm derivatives randomized at specific anchor positions. The results indicate that Qa-1b can bind a diverse repertoire of peptides but that Qdm has an optimal primary structure for binding Qa-1b. Flow cytometry experiments with Qa-1b tetramers and NK target cell lysis assays demonstrated that CD94/NKG2A discriminates between Qa-1b complexes containing peptides with substitutions at nonanchor positions P4, P5, or P8. Our findings suggest that it may be difficult for viruses to generate decoy peptides that mimic Qdm and raise the possibility that competitive replacement of Qdm with other peptides may provide a novel mechanism for activation of NK cells.

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11

Fukugita, M., H. Kawai, T. Nakazawa, and Y. Okamoto. "Monte Carlo simulation for folded structure of peptides." Nuclear Physics B - Proceedings Supplements 20 (May 1991): 766–70. http://dx.doi.org/10.1016/0920-5632(91)91018-f.

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12

Kelil, Abdellali, Emmanuel D. Levy, and Stephen W. Michnick. "Evolution of domain–peptide interactions to coadapt specificity and affinity to functional diversity." Proceedings of the National Academy of Sciences 113, no. 27 (June 17, 2016): E3862—E3871. http://dx.doi.org/10.1073/pnas.1518469113.

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Evolution of complexity in eukaryotic proteomes has arisen, in part, through emergence of modular independently folded domains mediating protein interactions via binding to short linear peptides in proteins. Over 30 years, structural properties and sequence preferences of these peptides have been extensively characterized. Less successful, however, were efforts to establish relationships between physicochemical properties and functions of domain–peptide interactions. To our knowledge, we have devised the first strategy to exhaustively explore the binding specificity of protein domain–peptide interactions. We applied the strategy to SH3 domains to determine the properties of their binding peptides starting from various experimental data. The strategy identified the majority (∼70%) of experimentally determined SH3 binding sites. We discovered mutual relationships among binding specificity, binding affinity, and structural properties and evolution of linear peptides. Remarkably, we found that these properties are also related to functional diversity, defined by depth of proteins within hierarchies of gene ontologies. Our results revealed that linear peptides evolved to coadapt specificity and affinity to functional diversity of domain–peptide interactions. Thus, domain–peptide interactions follow human-constructed gene ontologies, which suggest that our understanding of biological process hierarchies reflect the way chemical and thermodynamic properties of linear peptides and their interaction networks, in general, have evolved.

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Huang, Cheng-Hsin, Tong Wai Wong, Chen-Hsu Yu, Jing-Yuan Chang, Shing-Jong Huang, Shou-Ling Huang, and Richard P. Cheng. "Swapping the Positions in a Cross-Strand Lateral Ion-Pairing Interaction between Ammonium- and Carboxylate-Containing Residues in a β-Hairpin." Molecules 26, no. 5 (March 3, 2021): 1346. http://dx.doi.org/10.3390/molecules26051346.

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Cross-strand lateral ion-pairing interactions are important for antiparallel β-sheet stability. Statistical studies suggested that swapping the position of cross-strand lateral residues should not significantly affect the interaction. Herein, we swapped the position of ammonium- and carboxylate-containing residues with different side-chain lengths in a cross-strand lateral ion-pairing interaction in a β-hairpin. The peptides were analyzed by 2D-NMR. The fraction folded population and folding free energy were derived from the chemical shift data. The ion-pairing interaction energy was derived using double mutant cycle analysis. The general trends for the fraction folded population and interaction energetics remained similar upon swapping the position of the interacting charged residues. The most stabilizing cross-strand interactions were between short residues, similar to the unswapped study. However, the fraction folded populations for most of the swapped peptides were higher compared to the corresponding unswapped peptides. Furthermore, subtle differences in the ion-pairing interaction energy upon swapping were observed, most likely due to the “unleveled” relative positioning of the interacting residues created by the inherent right-handed twist of the structure. These results should be useful for developing functional peptides that rely on lateral ion-pairing interactions across antiparallel β-strands.

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Yap, Kuok, Junqiao Du, Fong Yang Looi, Shyn Ric Tang, Simon J. de Veer, Anuja R. Bony, Fabian B. H. Rehm, et al. "An environmentally sustainable biomimetic production of cyclic disulfide-rich peptides." Green Chemistry 22, no. 15 (2020): 5002–16. http://dx.doi.org/10.1039/d0gc01366h.

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Huang, Xueting, Chia-Hung Christine Hsiao, and Andrew J. Wiemer. "Discovery of TIGIT inhibitors by phage display." Journal of Immunology 210, no. 1_Supplement (May 1, 2023): 62.06. http://dx.doi.org/10.4049/jimmunol.210.supp.62.06.

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Abstract TIGIT is an emerging immune checkpoint receptor expressed higher than PD-1 in some tumors especially anti-PD1 resistant tumors. By competing with the co-stimulatory receptor CD226/DNAM-1 for binding to CD155/PVR, TIGIT transduces inhibitory signals and suppresses the immune response. Therefore, we sought to discover TIGIT inhibitors for improving tumor immunotherapy. Through directional cloning, bacterial transformation and phage amplification techniques, we generated a novel genetically encoded, phage-displayed bicyclic peptide library comprised of more than a million peptide sequences. Depending on the two combinations of different disulfide bonds, each peptide backbone is predicted to be folded into either endo-bicyclic or exo-bicyclic structure. We conducted three rounds of phage display panning against recombinant TIGIT IgV domain that enriched high-affinity peptides and identified promising TIGIT binding peptides. Phage ELISA showed binding of phage-presented peptides to recombinant TIGIT IgV and competitive ELISA evaluated the ability of the peptides to disrupt interactions between TIGIT and PVR. This work validated the efficiency of the phage-displayed bicyclic peptide library for discovery of ligands targeting protein receptors and led to identification of novel TIGIT inhibitors. AAI Careers in Immunology Fellowship

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Niu, Hongyan, Meng-Ying Li, Yi-Lun Ying, and Yi-Tao Long. "An engineered third electrostatic constriction of aerolysin to manipulate heterogeneously charged peptide transport." Chemical Science 13, no. 8 (2022): 2456–61. http://dx.doi.org/10.1039/d1sc06459b.

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Chakraborty, T. K., S. Jayaprakash, P. V. Diwan, R. Nagaraj, S. R. B. Jampani, and A. C. Kunwar. "Folded Conformation in Peptides Containing Furanoid Sugar Amino Acids." Journal of the American Chemical Society 120, no. 49 (December 1998): 12962–63. http://dx.doi.org/10.1021/ja9816685.

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Cline, Lauren L., and Marcey L. Waters. "The structure of well-folded Î²-hairpin peptides promotes resistance to peptidase degradation." Biopolymers 92, no. 6 (2009): 502–7. http://dx.doi.org/10.1002/bip.21266.

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Hunter, Howard N., A. Ross Demcoe, Håvard Jenssen, Tore J. Gutteberg, and Hans J. Vogel. "Human Lactoferricin Is Partially Folded in Aqueous Solution and Is Better Stabilized in a Membrane Mimetic Solvent." Antimicrobial Agents and Chemotherapy 49, no. 8 (August 2005): 3387–95. http://dx.doi.org/10.1128/aac.49.8.3387-3395.2005.

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ABSTRACT Lactoferricins are highly basic bioactive peptides that are released in the stomach through proteolytic cleavage of various lactoferrin proteins. Here we have determined the solution structure of human lactoferricin (LfcinH) by conventional two-dimensional nuclear magnetic resonance methods in both aqueous solution and a membrane mimetic solvent. Unlike the 25-residue bovine lactoferricin (LfcinB), which adopts a somewhat distorted antiparallel β sheet, the longer LfcinH peptide shows a helical content from Gln14 to Lys29 in the membrane mimetic solvent but a nonexistent β-sheet character in either the N- or C-terminal regions of the peptide. The helical characteristic of the LfcinH peptide resembles the conformation that this region adopts in the crystal structure of the intact protein. The LfcinH structure determined in aqueous solution displays a nascent helix in the form of a coiled conformation in the region from Gln14 to Lys29. Numerous hydrophobic interactions create the basis for the better-defined overall structure observed in the membrane mimetic solvent. The 49-residue LfcinH peptide isolated for these studies was found to be slightly longer than previously reported peptide preparations and was found to have an intact peptide bond between residues Ala11 and Val12. The distinct solution structures of LfcinH and LfcinB represent a novel difference in the physical properties of these two peptides, which contributes to their unique physiological activities.

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Sargent, F. "The twin-arginine transport system: moving folded proteins across membranes." Biochemical Society Transactions 35, no. 5 (October 25, 2007): 835–47. http://dx.doi.org/10.1042/bst0350835.

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The Tat (twin-arginine transport) pathway is a protein-targeting system dedicated to the transmembrane translocation of fully folded proteins. This system is highly prevalent in the cytoplasmic membranes of bacteria and archaea, and is also found in the thylakoid membranes of plant chloroplasts and possibly also in the inner membrane of plant mitochondria. Proteins are targeted to a membrane-embedded Tat translocase by specialized N-terminal twin-arginine signal peptides bearing an SRRXFLK amino acid motif. The genes encoding components of the Tat translocase were discovered approx. 10 years ago, and, since then, research in this area has expanded on a global scale. In this review, the key discoveries in this field are summarized, and recent studies of bacterial twin-arginine signal-peptide-binding proteins are discussed.

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21

Kotrba, Pavel, Lucie Dolečková, Víctor de Lorenzo, and Tomas Ruml. "Enhanced Bioaccumulation of Heavy Metal Ions by Bacterial Cells Due to Surface Display of Short Metal Binding Peptides." Applied and Environmental Microbiology 65, no. 3 (March 1, 1999): 1092–98. http://dx.doi.org/10.1128/aem.65.3.1092-1098.1999.

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ABSTRACT Metal binding peptides of sequences Gly-His-His-Pro-His-Gly (named HP) and Gly-Cys-Gly-Cys-Pro-Cys-Gly-Cys-Gly (named CP) were genetically engineered into LamB protein and expressed in Escherichia coli. The Cd2+-to-HP and Cd2+-to-CP stoichiometries of peptides were 1:1 and 3:1, respectively. Hybrid LamB proteins were found to be properly folded in the outer membrane ofE. coli. Isolated cell envelopes of E. colibearing newly added metal binding peptides showed an up to 1.8-fold increase in Cd2+ binding capacity. The bioaccumulation of Cd2+, Cu2+, and Zn2+ by E. coli was evaluated. Surface display of CP multiplied the ability of E. coli to bind Cd2+ from growth medium fourfold. Display of HP peptide did not contribute to an increase in the accumulation of Cu2+ and Zn2+. However, Cu2+ ceased contribution of HP for Cd2+accumulation, probably due to the strong binding of Cu2+ to HP. Thus, considering the cooperation of cell structures with inserted peptides, the relative affinities of metal binding peptide and, for example, the cell wall to metal ion should be taken into account in the rational design of peptide sequences possessing specificity for a particular metal.

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Chen, Charles H., Jakob P. Ulmschneider, and Martin B. Ulmschneider. "Mechanisms of a Small Membrane-Active Antimicrobial Peptide from Hyla punctata." Australian Journal of Chemistry 73, no. 3 (2020): 236. http://dx.doi.org/10.1071/ch19429.

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Thousands of antimicrobial peptides have been observed and studied in the past decades; however, their membrane-active mechanisms are ambiguous due to their dynamic structure in the cell membrane. Here, we applied both molecular dynamics (MD) simulations and biophysical experiments to study the small membrane-active antimicrobial peptide Hylaseptin P1 (HSP1), which has significant selectivity towards anionic 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1′-rac-glycerol) (POPG) and bacterial model membranes. HSP1 does not bind and fold onto human red blood cell model membranes, and it only binds, but does not fold, in zwitterionic 1-palmitoyl-2-oleoyl-glycero-3-phosphocholine (POPC) membranes. This suggests that the lipid chemistry and membrane rigidity are key to prevent HSP1 binding onto membranes, and the lipid headgroup charge may further promote peptide folding in the membrane. Our experiment-validated MD simulations suggest a carpet-like model mechanism for HSP1 through peptide binding, folding, aggregation, and assembly. HSP1 is shorter than the membrane thickness; therefore, the folded peptides aggregate on the surface, cross the membrane, and the oligomeric structure is supported by several surface-bound peptides in both bilayer leaflets.

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Khvotchev, Mikhail, and Mikhail Soloviev. "SNARE Modulators and SNARE Mimetic Peptides." Biomolecules 12, no. 12 (November 29, 2022): 1779. http://dx.doi.org/10.3390/biom12121779.

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The soluble N-ethylmaleimide-sensitive factor (NSF) attachment protein (SNAP) receptor (SNARE) proteins play a central role in most forms of intracellular membrane trafficking, a key process that allows for membrane and biocargo shuffling between multiple compartments within the cell and extracellular environment. The structural organization of SNARE proteins is relatively simple, with several intrinsically disordered and folded elements (e.g., SNARE motif, N-terminal domain, transmembrane region) that interact with other SNAREs, SNARE-regulating proteins and biological membranes. In this review, we discuss recent advances in the development of functional peptides that can modify SNARE-binding interfaces and modulate SNARE function. The ability of the relatively short SNARE motif to assemble spontaneously into stable coiled coil tetrahelical bundles has inspired the development of reduced SNARE-mimetic systems that use peptides for biological membrane fusion and for making large supramolecular protein complexes. We evaluate two such systems, based on peptide-nucleic acids (PNAs) and coiled coil peptides. We also review how the self-assembly of SNARE motifs can be exploited to drive on-demand assembly of complex re-engineered polypeptides.

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Li, Nian-Zhi, Chen-Hsu Yu, Jhuan-Yu Wu, Shing-Jong Huang, Shou-Ling Huang, and Richard P. Cheng. "Diagonal Interactions between Glutamate and Arginine Analogs with Varying Side-Chain Lengths in a β-Hairpin." Molecules 28, no. 7 (March 23, 2023): 2888. http://dx.doi.org/10.3390/molecules28072888.

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Cross-strand interactions are important for the stability of β-sheet structures. Accordingly, cross-strand diagonal interactions between glutamate and arginine analogs with varying side-chain lengths were studied in a series of β-hairpin peptides. The peptides were analyzed by homonuclear two-dimensional nuclear magnetic resonance methods. The fraction folded population and folding free energy of the peptides were derived from the chemical shift data. The fraction folded population trends could be rationalized using the strand propensity of the constituting residues, which was not the case for the peptides with lysine analogs, highlighting the difference between the arginine analogs and lysine analogs. Double-mutant cycle analysis was used to derive the diagonal ion-pairing interaction energetics. The most stabilizing diagonal cross-strand interaction was between the shortest residues (i.e., Asp2–Agp9), most likely due to the least side-chain conformational penalty for ion-pair formation. The diagonal interaction energetics in this study involving the arginine analogs appears to be consistent with and extend beyond our understanding of diagonal ion-pairing interactions involving lysine analogs. The results should be useful for designing β-strand-containing molecules to affect biological processes such as amyloid formation and protein-protein interactions.

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Wynn, Jessica E., and Webster L. Santos. "HIV-1 drug discovery: targeting folded RNA structures with branched peptides." Organic & Biomolecular Chemistry 13, no. 21 (2015): 5848–58. http://dx.doi.org/10.1039/c5ob00589b.

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Petkov, Peicho, Elena Lilkova, Nevena Ilieva, and Leandar Litov. "Self-Association of Antimicrobial Peptides: A Molecular Dynamics Simulation Study on Bombinin." International Journal of Molecular Sciences 20, no. 21 (November 1, 2019): 5450. http://dx.doi.org/10.3390/ijms20215450.

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Antimicrobial peptides (AMPs) are a diverse group of membrane-active peptides which play a crucial role as mediators of the primary host defense against microbial invasion. Many AMPs are found to be fully or partially disordered in solution and to acquire secondary structure upon interaction with a lipid membrane. Here, we report molecular dynamics simulations studies on the solution behaviour of a specific AMP, bombinin H2. We show that in monomeric form in water solution the peptide is somewhat disordered and preferably adopts a helix-loop-helix conformation. However, when more than a single monomer is placed in the solution, the peptides self-associate in aggregates. Within the aggregate, the peptides provide each other with an amphipathic environment that mimics the water–membrane interface, which allows them to adopt a single-helix structure. We hypothesise that this is the mechanism by which bombinin H2 and, possibly, other small linear AMPs reach the target membrane in a functional folded state and are able to effectively exert their antimicrobial action on it.

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Natarajan, Kannan, Jiansheng Jiang, Lisa F. Boyd, Giora I. Morozov, Michael G. Mage, and David H. Margulies. "Insights into MHC-I peptide loading obtained from the structure of a TAPBPR/MHC-I complex." Journal of Immunology 198, no. 1_Supplement (May 1, 2017): 146.25. http://dx.doi.org/10.4049/jimmunol.198.supp.146.25.

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Abstract The cell surface expression of MHC-I molecules displaying peptides derived from intracellular proteolytic processing is a critical requirement for T cell-mediated immunity. A complex series of steps, guided by the peptide loading machinery in the endoplasmic reticulum, ensures that only stably folded MHC-I molecules carrying peptides of proper length and high affinity are transported for display at the cell surface. TAP-binding protein, related (TAPBPR), has been recently shown to directly bind to certain MHC-I alleles and to facilitate peptide loading. To elucidate mechanistic details, we have examined the binding interaction between purified recombinant TAPBPR and MHC-I molecules loaded with truncated peptides that leave a portion of the peptide binding groove unoccupied. Such MHC-I molecules interact with TAPBPR with nanomolar affinities as measured by surface plasmon resonance and these TAPBPR/MHC-I complexes dissociate when offered a high affinity peptide. An extensive crystallization screen with purified TAPBPR/MHC-I complexes yielded crystals that diffracted to 3.5 Å. The structure of the TAPBPR/MHC-I complex, solved by molecular replacement, and refined at this resolution readily reveals the binding footprint and further structural details of the interaction. Data will be presented on the binding interaction and structural characterization of the TAPBPR/MHC-I complex that reveal insights into the mechanism of TAPBPR- and tapasin-mediated loading of peptides onto MHC-I molecules. (KN and JJ contributed equally to this work).

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Chang, Jing-Yuan, Yen-Jin Pan, Pei-Yu Huang, Yi-Ting Sun, Chen-Hsu Yu, Zhi-Jun Ning, Shou-Ling Huang, Shing-Jong Huang, and Richard P. Cheng. "The Effects of Charged Amino Acid Side-Chain Length on Diagonal Cross-Strand Interactions between Carboxylate- and Ammonium-Containing Residues in a β-Hairpin." Molecules 27, no. 13 (June 29, 2022): 4172. http://dx.doi.org/10.3390/molecules27134172.

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The β-sheet is one of the common protein secondary structures, and the aberrant aggregation of β-sheets is implicated in various neurodegenerative diseases. Cross-strand interactions are an important determinant of β-sheet stability. Accordingly, both diagonal and lateral cross-strand interactions have been studied. Surprisingly, diagonal cross-strand ion-pairing interactions have yet to be investigated. Herein, we present a systematic study on the effects of charged amino acid side-chain length on a diagonal ion-pairing interaction between carboxylate- and ammonium-containing residues in a β-hairpin. To this end, 2D-NMR was used to investigate the conformation of the peptides. The fraction folded population and the folding free energy were derived from the chemical shift data. The fraction folded population for these peptides with potential diagonal ion pairs was mostly lower compared to the corresponding peptide with a potential lateral ion pair. The diagonal ion-pairing interaction energy was derived using double mutant cycle analysis. The Asp2-Dab9 (Asp: one methylene; Dab: two methylenes) interaction was the most stabilizing (−0.79 ± 0.14 kcal/mol), most likely representing an optimal balance between the entropic penalty to enable the ion-pairing interaction and the number of side-chain conformations that can accommodate the interaction. These results should be useful for designing β-sheet containing molecular entities for various applications.

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Barre, Annick, Hervé Benoist, and Pierre Rougé. "Impacts of Sourdough Technology on the Availability of Celiac Peptides from Wheat α- and γ-Gliadins: In Silico Approach." Allergies 3, no. 1 (February 3, 2023): 39–57. http://dx.doi.org/10.3390/allergies3010004.

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Celiac peptide-generating α- and γ-gliadins consist of a disordered N-terminal domain extended by an α-helical-folded C-terminal domain. Celiac peptides, primarily located along the disordered part of α- and γ-gliadin molecules, are nicely exposed and directly accessible to proteolytic enzymes occurring in the gastric (pepsin) and intestinal (trypsin, chymotrypsin) fluids. More than half of the potential celiac peptides identified so far in gliadins exhibit cleavage sites for pepsin. However, celiac peptides proteolytically truncated by one or two amino acid residues could apparently retain some activity toward HLA-DQ2 and HLA-DQ8 receptors in docking experiments. Together with the uncleaved peptides, these still active partially degraded CD peptides account for the incapacity of the digestion process to inactivate CD peptides from gluten proteins. In contrast, sourdough fermentation processes involve other proteolytic enzymes susceptible to the deep degradation of celiac peptides. In particular, sourdough supplemented by fungal prolyl endoproteases enhances the degrading capacities of the sourdough fermentation process toward celiac peptides. Nevertheless, since tiny amounts of celiac peptides sufficient to trigger deleterious effects on CD people can persist in sourdough-treated bread and food products, it is advisable to avoid consumption of sourdough-treated food products for people suffering from celiac disease. As an alternative, applying the supplemented sourdough process to genetically modified low gluten or celiac-safe wheat lines should result in food products that are safer for susceptible and CD people.

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Taubert, Johannes, and Thomas Brüser. "Twin-arginine translocation-arresting protein regions contact TatA and TatB." Biological Chemistry 395, no. 7-8 (July 1, 2014): 827–36. http://dx.doi.org/10.1515/hsz-2014-0170.

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Abstract Tat systems translocate folded proteins across biological membranes of prokaryotes and plant plastids. TatBC complexes recognize N-terminal Tat signal peptides that contain a sequence motif with two conserved arginines (RR-motif), and transport takes place after a recruitment of TatA. Unfolded Tat substrate domains lower translocation efficiency and too long linkers lead to translocation arrest. To identify the components that interact with transported proteins during their passage through the translocon, we used a Tat substrate that arrests translocation at a long unfolded linker region, and we chose in vivo site-directed photo cross-linking to specifically detect the interactions of this linker region. For comparison, we included the interactions of the signal peptide and of the folded domain at the C-terminus of this construct. The data show that the linker contacts only two, structurally similar Tat components, namely TatA and TatB. These contacts depend on the recognition of the Tat-specific signal peptide. Only when membrane translocation of the globular domain was allowed – i.e., in the absence of the linker – we observed the same TatAB-contacts also to the globular domain. The data thus suggest that mature protein domains are translocated through a TatAB environment.

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Zhai, Luhan, Masayuki Nara, Yuko Otani, and Tomohiko Ohwada. "Unexpectedly rigid short peptide foldamers in which NH–π and CH–π interactions are preserved in solution." Chemical Communications 57, no. 67 (2021): 8344–47. http://dx.doi.org/10.1039/d1cc02998c.

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We found that a group of short peptides with only three amino acids containing a phenylalanine formed highly stable folded structures in solution, wherein CH–π and NH–π main chain–side chain interactions can be clearly observed by NMR and ATR-IR.

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Huang, Qi, Felicity Alcock, Holger Kneuper, Justin C. Deme, Sarah E. Rollauer, Susan M. Lea, Ben C. Berks, and Tracy Palmer. "A signal sequence suppressor mutant that stabilizes an assembled state of the twin arginine translocase." Proceedings of the National Academy of Sciences 114, no. 10 (February 21, 2017): E1958—E1967. http://dx.doi.org/10.1073/pnas.1615056114.

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The twin-arginine protein translocation (Tat) system mediates transport of folded proteins across the cytoplasmic membrane of bacteria and the thylakoid membrane of chloroplasts. The Tat system ofEscherichia coliis made up of TatA, TatB, and TatC components. TatBC comprise the substrate receptor complex, and active Tat translocases are formed by the substrate-induced association of TatA oligomers with this receptor. Proteins are targeted to TatBC by signal peptides containing an essential pair of arginine residues. We isolated substitutions, locating to the transmembrane helix of TatB that restored transport activity to Tat signal peptides with inactivating twin arginine substitutions. A subset of these variants also suppressed inactivating substitutions in the signal peptide binding site on TatC. The suppressors did not function by restoring detectable signal peptide binding to the TatBC complex. Instead, site-specific cross-linking experiments indicate that the suppressor substitutions induce conformational change in the complex and movement of the TatB subunit. The TatB F13Y substitution was associated with the strongest suppressing activity, even allowing transport of a Tat substrate lacking a signal peptide. In vivo analysis using a TatA–YFP fusion showed that the TatB F13Y substitution resulted in signal peptide-independent assembly of the Tat translocase. We conclude that Tat signal peptides play roles in substrate targeting and in triggering assembly of the active translocase.

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Byazrova, Maria, Pia Gattinger, Ekaterina Astakhova, Gerhard Hofer, Musa Khaitov, Alexander Filatov, and Rudolf Valenta. "Dissection of Antibody Responses of Gam-COVID-Vac-Vaccinated Subjects Suggests Involvement of Epitopes Outside RBD in SARS-CoV-2 Neutralization." International Journal of Molecular Sciences 24, no. 6 (March 7, 2023): 5104. http://dx.doi.org/10.3390/ijms24065104.

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Millions of people have been vaccinated with Gam-COVID-Vac but fine specificities of induced antibodies have not been fully studied. Plasma from 12 naïve and 10 coronavirus disease 2019 (COVID-19) convalescent subjects was obtained before and after two immunizations with Gam-COVID-Vac. Antibody reactivity in the plasma samples (n = 44) was studied on a panel of micro-arrayed recombinant folded and unfolded severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) proteins and 46 peptides spanning the spike protein (S) and by immunoglobulin G (IgG) subclass enzyme-linked immunosorbent assay (ELISA). The ability of Gam-COVID-Vac-induced antibodies to inhibit binding of the receptor-binding domain (RBD) to its receptor angiotensin converting enzyme 2 (ACE2) was investigated in a molecular interaction assay (MIA). The virus-neutralizing capacity of antibodies was studied by the pseudo-typed virus neutralization test (pVNT) for Wuhan-Hu-1 and Omicron. We found that Gam-COVID-Vac vaccination induced significant increases of IgG1 but not of other IgG subclasses against folded S, spike protein subunit 1 (S1), spike protein subunit 2 (S2), and RBD in a comparable manner in naïve and convalescent subjects. Virus neutralization was highly correlated with vaccination-induced antibodies specific for folded RBD and a novel peptide (i.e., peptide 12). Peptide 12 was located close to RBD in the N-terminal part of S1 and may potentially be involved in the transition of the pre- to post-fusion conformation of the spike protein. In summary, Gam-COVID-Vac vaccination induced S-specific IgG1 antibodies in naive and convalescent subjects in a comparable manner. Besides the antibodies specific for RBD, the antibodies induced against a peptide close to the N-terminus of RBD were also associated with virus-neutralization.

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Misra, Rajkumar, Rahi M. Reja, Lagumaddepalli V. Narendra, Gijo George, Srinivasarao Raghothama, and Hosahudya N. Gopi. "Exploring structural features of folded peptide architectures in the construction of nanomaterials." Chemical Communications 52, no. 61 (2016): 9597–600. http://dx.doi.org/10.1039/c6cc04502b.

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Ardejani, Maziar S., Evan T. Powers, and Jeffery W. Kelly. "Using Cooperatively Folded Peptides To Measure Interaction Energies and Conformational Propensities." Accounts of Chemical Research 50, no. 8 (July 19, 2017): 1875–82. http://dx.doi.org/10.1021/acs.accounts.7b00195.

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Schröder, Bernd, and Paul Saftig. "Molecular insights into mechanisms of intramembrane proteolysis through signal peptide peptidase (SPP)." Biochemical Journal 427, no. 3 (April 14, 2010): e1-e3. http://dx.doi.org/10.1042/bj20100391.

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The processing of membrane-anchored signalling molecules and transcription factors by RIP (regulated intramembrane proteolysis) is a major signalling paradigm in eukaryotic cells. Intramembrane cleaving proteases liberate fragments from membrane-bound precursor proteins which typically fulfil functions such as cell signalling and regulation, immunosurveillance and intercellular communication. Furthermore, they are thought to be involved in the development and propagation of several diseases, such as Alzheimer's disease and hepatitis C virus infection. In this issue of the Biochemical Journal, Schrul and colleagues investigate the interaction of the endoplasmic reticulum-resident intramembrane cleaving SPP (signal peptide peptidase) with different type II oriented transmembrane proteins. A combination of co-immunoprecipitation experiments using wild-type and a dominant-negative SPP with electrophoretic protein separations under native conditions revealed selectivity of the interaction. Depending on the interacting protein, SPP formed complexes of different sizes. SPP could build tight interactions not only with signal peptides, but also with pre- and mis-folded proteins. Whereas signal peptides are direct substrates for SPP proteolysis, the study suggests that SPP may be involved in the controlled sequestration of possibly toxic membrane protein species in a proteolysis-independent manner. These large oligomeric membrane protein aggregates may then be degraded by the proteasome or autophagy.

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Stroganova, Iuliia, Sjors Bakels, and Anouk M. Rijs. "Structural Properties of Phenylalanine-Based Dimers Revealed Using IR Action Spectroscopy." Molecules 27, no. 7 (April 6, 2022): 2367. http://dx.doi.org/10.3390/molecules27072367.

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Peptide segments with phenylalanine residues are commonly found in proteins that are related to neurodegenerative diseases. However, the self-assembly of phenylalanine-based peptides can be also functional. Peptides containing phenylalanine residues with different side caps, composition, and chemical alteration can form different types of nanostructures that find many applications in technology and medicine. Various studies have been performed in order to explain the remarkable stability of the resulting nanostructures. Here, we study the early stages of self-assembly of two phenylalanine derived peptides in the gas phase using IR action spectroscopy. Our focus lies on the identification of the key intra- and intermolecular interactions that govern the formation of the dimers. The far-IR region allowed us to distinguish between structural families and to assign the 2-(2-amino-2-phenylacetamido)-2-phenylacetic acid (PhgPhg) dimer to a very symmetric structure with two intermolecular hydrogen bonds and its aromatic rings folded away from the backbone. By comparison with the phenylalanine-based peptide cyclic L-phenylalanyl-L-phenylalanine (cyclo-FF), we found that the linear FF dimer likely adopts a less ordered structure. However, when one more phenylalanine residue is added (FFF), a more structurally organized dimer is formed with several intermolecular hydrogen bonds.

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Zhang, Huixi Violet, Frank Polzer, Michael J. Haider, Yu Tian, Jose A. Villegas, Kristi L. Kiick, Darrin J. Pochan, and Jeffery G. Saven. "Computationally designed peptides for self-assembly of nanostructured lattices." Science Advances 2, no. 9 (September 2016): e1600307. http://dx.doi.org/10.1126/sciadv.1600307.

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Folded peptides present complex exterior surfaces specified by their amino acid sequences, and the control of these surfaces offers high-precision routes to self-assembling materials. The complexity of peptide structure and the subtlety of noncovalent interactions make the design of predetermined nanostructures difficult. Computational methods can facilitate this design and are used here to determine 29-residue peptides that form tetrahelical bundles that, in turn, serve as building blocks for lattice-forming materials. Four distinct assemblies were engineered. Peptide bundle exterior amino acids were designed in the context of three different interbundle lattices in addition to one design to produce bundles isolated in solution. Solution assembly produced three different types of lattice-forming materials that exhibited varying degrees of agreement with the chosen lattices used in the design of each sequence. Transmission electron microscopy revealed the nanostructure of the sheetlike nanomaterials. In contrast, the peptide sequence designed to form isolated, soluble, tetrameric bundles remained dispersed and did not form any higher-order assembled nanostructure. Small-angle neutron scattering confirmed the formation of soluble bundles with the designed size. In the lattice-forming nanostructures, the solution assembly process is robust with respect to variation of solution conditions (pH and temperature) and covalent modification of the computationally designed peptides. Solution conditions can be used to control micrometer-scale morphology of the assemblies. The findings illustrate that, with careful control of molecular structure and solution conditions, a single peptide motif can be versatile enough to yield a wide range of self-assembled lattice morphologies across many length scales (1 to 1000 nm).

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Nayar, Divya, and Charusita Chakravarty. "Sensitivity of local hydration behaviour and conformational preferences of peptides to choice of water model." Phys. Chem. Chem. Phys. 16, no. 21 (2014): 10199–213. http://dx.doi.org/10.1039/c3cp55147d.

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Hallupp, M., F. Buck, and W. H. Strätling. "Structure analysis of purified histone H5 and of H5 in nuclei by limited proteolysis." Biochemical Journal 282, no. 2 (March 1, 1992): 435–41. http://dx.doi.org/10.1042/bj2820435.

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The structure of purified histone H5 in 1 M-NaClO4 and of H5 in nuclei was analysed by digestion with either one of three endoproteinases, papain, subtilisin or elastase, which preferentially cleave unstructured protein regions (and additionally with trypsin). Digestion with papain and subtilisin produced ‘limiting’ resistant peptides (p1 and s1) that contain the central region between residues 18-20 and residue 114. Digestion of purified H5 with elastase generated resistant peptides e1 and e2, and that of H5 in nuclei, peptide e2. Peptides e1 and e2 contain the region from residues 22 to 114 and 109 respectively. These results show that a central region of H5 encompassing the sequence between residues 18-22 and residue 114 is folded into a compact structure. A central structured ‘core’ domain ranging from residues 22 to 100 is defined by the limit trypsin peptide t3, which is identical to the previously described fragment GH5 [Aviles et al. (1978) Eur. J. Biochem. 88, 363-371]. Generation of peptides e2 and t3, as well as of resistant peptides of lower abundance, shows that the sites near Lys-100 and Lys-109 exhibit some proteolytic sensitivity, which may result either from an exposed location or from a locally less compact conformation. Significantly, all these structural features of H5 are manifested in the purified form as well as in nuclei. A role of the structured region from residues 101 to 114 for the interaction with linker DNA and the determination of its path is discussed.

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SOTERIADOU, Ketty P., Athina K. TZINIA, Evgenia PANOU-PAMONIS, Vassilias TSIKARIS, Maria SAKARELLOS-DAITSIOTIS, Constantinos SAKARELLOS, Youli PAPAPOULOU, and Rebecca MATSAS. "Antigenicity and conformational analysis of the Zn2+-binding sites of two Zn2+-metalloproteases: Leishmania gp63 and mammalian endopeptidase-24.11." Biochemical Journal 313, no. 2 (January 15, 1996): 455–66. http://dx.doi.org/10.1042/bj3130455.

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The antigenic properties of the Zn2+-binding region of two Zn2+-metalloproteases, Leishmania surface protease gp63 and mammalian endopeptidase-24.11 (E-24.11), possessing in their active site the characteristic amino acid sequence HEXXH, were investigated by using oligoclonal antibodies raised against two synthetic peptides, V1VTHEMAHALG11 (pepgp63) and V1IGHEITHGFD11 (pepE-24.11), containing the respective Zn2+-binding sites of the cognate protein. The affinity-purified antibodies, tested on synthetic peptides modelled from the active sites of ten different Zn2+-metalloproteases, showed high selectivity for their respective peptides. However, cross-reactivity was revealed when the antibodies were tested against the gp63 and E-24.11 molecules. A panel of synthetic peptide analogues and peptides of various size was synthesized and used for the fine antigenic characterization of pepgp63 and pepE-24.11. The shortest peptides capable of significant antibody binding were the pentapeptides V1VTHE5 and E5ITHG9 for pepgp63 and pepE-24.11 respectively. His4 and Glu5 were found to be indispensable for anti-pepgp63 binding to pepgp63, whereas in the case of pepE-24.11, Glu5 and His8 were found to be critical. The conformational characteristics of the two peptides correlate well with the observed differences in their antigenicity. 1H-NMR studies showed that pepgp63 adopts a folded structure whereas pepE-24.11 takes up a rather flexible conformation. Moreover, the antigenically critical His4 of pepgp63 contributes to the structural stabilization of the peptide. Similarly, the antigenically critical His8 of pepE-24.11 is involved in partial structural stabilization of its C-terminal region. The generated antibodies may be useful tools for identifying and classifying proteins possessing similar Zn2+-binding motifs and/or environments.

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Haris, P. I. "Structural model of a voltage-gated potassium channel based on spectroscopic data." Biochemical Society Transactions 29, no. 4 (August 1, 2001): 589–93. http://dx.doi.org/10.1042/bst0290589.

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It is estimated that membrane proteins comprise as much as 30% of most genomes. Yet our knowledge of membrane-protein folding is still in its infancy. Consequently, there is a great need for developing approaches that can further advance our understanding of how peptides and proteins interact with membranes and thereby attain their folded structure. An approach that we have been exploring involves dissecting voltage-gated ion channels into simple peptide domains for the purpose of determining their structure in different media using physical techniques. We have synthesized peptides corresponding to the six membrane-spanning segments, as well as the pore domain, of the Shaker channel and characterized their secondary structures. From these studies we have developed a model for the transmembrane structure of the Shaker potassium channel that is constructed from α-helices. The hard structural data obtained from these studies lends support to the recent theoretical models of this channel protein that have been developed by others.

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van der Ploeg, René, Carmine G. Monteferrante, Sjouke Piersma, James P. Barnett, Thijs R. H. M. Kouwen, Colin Robinson, and Jan Maarten van Dijl. "High-Salinity Growth Conditions Promote Tat-Independent Secretion of Tat Substrates in Bacillus subtilis." Applied and Environmental Microbiology 78, no. 21 (August 24, 2012): 7733–44. http://dx.doi.org/10.1128/aem.02093-12.

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ABSTRACTThe Gram-positive bacteriumBacillus subtiliscontains two Tat translocases, which can facilitate transport of folded proteins across the plasma membrane. Previous research has shown that Tat-dependent protein secretion inB. subtilisis a highly selective process and that heterologous proteins, such as the green fluorescent protein (GFP), are poor Tat substrates in this organism. Nevertheless, when expressed inEscherichia coli, bothB. subtilisTat translocases facilitated exclusively Tat-dependent export of folded GFP when the twin-arginine (RR) signal peptides of theE. coliAmiA, DmsA, or MdoD proteins were attached. Therefore, the present studies were aimed at determining whether the same RR signal peptide-GFP precursors would also be exported Tat dependently inB. subtilis. In addition, we investigated the secretion of GFP fused to the full-length YwbN protein, a strict Tat substrate inB. subtilis. Several investigated GFP fusion proteins were indeed secreted inB. subtilis, but this secretion was shown to be completely Tat independent. At high-salinity growth conditions, the Tat-independent secretion of GFP as directed by the RR signal peptides from theE. coliAmiA, DmsA, or MdoD proteins was significantly enhanced, and this effect was strongest in strains lacking the TatAy-TatCy translocase. This implies that high environmental salinity has a negative influence on the avoidance of Tat-independent secretion of AmiA-GFP, DmsA-GFP, and MdoD-GFP. We conclude that as-yet-unidentified control mechanisms reject the investigated GFP fusion proteins for translocation by theB. subtilisTat machinery and, at the same time, set limits to their Tat-independent secretion, presumably via the Sec pathway.

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Woodhead, Andrea, Andrew Church, Trevor Rapson, Holly Trueman, Jeffrey Church, and Tara Sutherland. "Confirmation of Bioinformatics Predictions of the Structural Domains in Honeybee Silk." Polymers 10, no. 7 (July 16, 2018): 776. http://dx.doi.org/10.3390/polym10070776.

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Honeybee larvae produce a silk made up of proteins in predominantly a coiled coil molecular structure. These proteins can be produced in recombinant systems, making them desirable templates for the design of advanced materials. However, the atomic level structure of these proteins is proving difficult to determine: firstly, because coiled coils are difficult to crystalize; and secondly, fibrous proteins crystalize as fibres rather than as discrete protein units. In this study, we synthesised peptides from the central structural domain, as well as the N- and C-terminal domains, of the honeybee silk. We used circular dichroism spectroscopy, infrared spectroscopy, and molecular dynamics to investigate the folding behaviour of the central domain peptides. We found that they folded as predicted by bioinformatics analysis, giving the protein engineer confidence in bioinformatics predictions to guide the design of new functionality into these protein templates. These results, along with the infrared structural analysis of the N- and C-terminal domain peptides and the comparison of peptide film properties with those of the full-length AmelF3 protein, provided significant insight into the structural elements required for honeybee silk protein to form into stable materials.

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Lukacik, Petra, C. David Owen, Gemma Harris, Jani Reddy Bolla, Sarah Picaud, Irfan Alibay, Joanne E. Nettleship, et al. "The structure of nontypeable Haemophilus influenzae SapA in a closed conformation reveals a constricted ligand-binding cavity and a novel RNA binding motif." PLOS ONE 16, no. 10 (October 15, 2021): e0256070. http://dx.doi.org/10.1371/journal.pone.0256070.

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Nontypeable Haemophilus influenzae (NTHi) is a significant pathogen in respiratory disease and otitis media. Important for NTHi survival, colonization and persistence in vivo is the Sap (sensitivity to antimicrobial peptides) ABC transporter system. Current models propose a direct role for Sap in heme and antimicrobial peptide (AMP) transport. Here, the crystal structure of SapA, the periplasmic component of Sap, in a closed, ligand bound conformation, is presented. Phylogenetic and cavity volume analysis predicts that the small, hydrophobic SapA central ligand binding cavity is most likely occupied by a hydrophobic di- or tri- peptide. The cavity is of insufficient volume to accommodate heme or folded AMPs. Crystal structures of SapA have identified surface interactions with heme and dsRNA. Heme binds SapA weakly (Kd 282 μM) through a surface exposed histidine, while the dsRNA is coordinated via residues which constitute part of a conserved motif (estimated Kd 4.4 μM). The RNA affinity falls within the range observed for characterized RNA/protein complexes. Overall, we describe in molecular-detail the interactions of SapA with heme and dsRNA and propose a role for SapA in the transport of di- or tri-peptides.

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Lehmann, T. E., G. Kroon, H. J. Dyson, M. A. Lorenzo, H. Bermúdez, and H. Perez. "Plasmodium vivax CS peptides display conformational preferences for folded forms in solution." Journal of Peptide Research 61, no. 5 (March 28, 2003): 252–62. http://dx.doi.org/10.1034/j.1399-3011.2003.00055.x.

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Haridas, V., Sandhya Sadanandan, M. V. S. Gopalakrishna, M. B. Bijesh, Ram P. Verma, Srinivas Chinthalapalli, and Ashutosh Shandilya. "Bispidine as a helix inducing scaffold: examples of helically folded linear peptides." Chemical Communications 49, no. 93 (2013): 10980. http://dx.doi.org/10.1039/c3cc45649h.

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Bhattacharjya, Surajit, Padmanabhan Balaram, Satish K. Awasthi, and P. Radhakantha Adiga. "Folded conformations of antigenic peptides from riboflavin carrier protein in aqueous hexafluoroacetone." Protein Science 7, no. 1 (January 1998): 123–31. http://dx.doi.org/10.1002/pro.5560070113.

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Wani, Naiem Ahmad, Vivek Kumar Gupta, Umesh Prasad Singh, Subrayashastry Aravinda, and Rajkishor Rai. "Folded Structure Stabilized by C7, C10and C12Hydrogen Bonds in αγ Hybrid Peptides." ChemistrySelect 1, no. 8 (June 1, 2016): 1674–77. http://dx.doi.org/10.1002/slct.201600389.

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Dröge, Melloney J., Ykelien L. Boersma, Peter G. Braun, Robbert Jan Buining, Mattijs K. Julsing, Karin G. A. Selles, Jan Maarten van Dijl, and Wim J. Quax. "Phage Display of an Intracellular Carboxylesterase of Bacillus subtilis: Comparison of Sec and Tat Pathway Export Capabilities." Applied and Environmental Microbiology 72, no. 7 (July 2006): 4589–95. http://dx.doi.org/10.1128/aem.02750-05.

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ABSTRACT Using the phage display technology, a protein can be displayed at the surface of bacteriophages as a fusion to one of the phage coat proteins. Here we describe development of this method for fusion of an intracellular carboxylesterase of Bacillus subtilis to the phage minor coat protein g3p. The carboxylesterase gene was cloned in the g3p-based phagemid pCANTAB 5E upstream of the sequence encoding phage g3p and downstream of a signal peptide-encoding sequence. The phage-bound carboxylesterase was correctly folded and fully enzymatically active, as determined from hydrolysis of the naproxen methyl ester with Km values of 0.15 mM and 0.22 mM for the soluble and phage-displayed carboxylesterases, respectively. The signal peptide directs the encoded fusion protein to the cell membrane of Escherichia coli, where phage particles are assembled. In this study, we assessed the effects of several signal peptides, both Sec dependent and Tat dependent, on the translocation of the carboxylesterase in order to optimize the phage display of this enzyme normally restricted to the cytoplasm. Functional display of Bacillus carboxylesterase NA could be achieved when Sec-dependent signal peptides were used. Although a Tat-dependent signal peptide could direct carboxylesterase translocation across the inner membrane of E. coli, proper assembly into phage particles did not seem to occur.

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Journal articles on the topic 'Folded Peptides'

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