Journal articles on the topic 'Membrane proteins and peptides'
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1
Schrul, Bianca, Katja Kapp, Irmgard Sinning, and Bernhard Dobberstein. "Signal peptide peptidase (SPP) assembles with substrates and misfolded membrane proteins into distinct oligomeric complexes." Biochemical Journal 427, no. 3 (April 14, 2010): 523–34. http://dx.doi.org/10.1042/bj20091005.
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SPP (signal peptide peptidase) is an aspartyl intramembrane cleaving protease, which processes a subset of signal peptides, and is linked to the quality control of ER (endoplasmic reticulum) membrane proteins. We analysed SPP interactions with signal peptides and other membrane proteins by co-immunoprecipitation assays. We found that SPP interacts specifically and tightly with a large range of newly synthesized membrane proteins, including signal peptides, preproteins and misfolded membrane proteins, but not with all co-expressed type II membrane proteins. Signal peptides are trapped by the catalytically inactive SPP mutant SPPD/A. Preproteins and misfolded membrane proteins interact with both SPP and the SPPD/A mutant, and are not substrates for SPP-mediated intramembrane proteolysis. Proteins interacting with SPP are found in distinct complexes of different sizes. A signal peptide is mainly trapped in a 200 kDa SPP complex, whereas a preprotein is predominantly found in a 600 kDa SPP complex. A misfolded membrane protein is detected in 200, 400 and 600 kDa SPP complexes. We conclude that SPP not only processes signal peptides, but also collects preproteins and misfolded membrane proteins that are destined for disposal.
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Martin, Isabelle, and Jean-Marie Ruysschaert. "Common Properties of Fusion Peptides from Diverse Systems." Bioscience Reports 20, no. 6 (December 1, 2000): 483–500. http://dx.doi.org/10.1023/a:1010454803579.
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Although membrane fusion occurs ubiquitously and continuously in alleukaroytic cells, little is known about the mechanism that governs lipidbilayer fusion associated with any intracellular fusion reactions. Recentstudies of the fusion of enveloped viruses with host cell membranes havehelped to define the fusion process. The identification and characterizationof key proteins involved in fusion reactions have mainly driven recent advancesin our understanding of membrane fusion. The most important denominator amongthe fusion proteins is the fusion peptide. In this review, work done in thelast few years on the molecular mechanism of viral membrane fusion will behighlighted, focusing in particular on the role of the fusion peptide and themodification of the lipid bilayer structure. Much of what is known regardingthe molecular mechanism of viral membrane fusion has been gained using liposomesas model systems in which the molecular components of the membrane and the environmentare strictly controlled. Many amphilphilic peptides have a high affinity forlipid bilayers, but only a few sequences are able to induce membrane fusion. Thepresence of α-helical structure in at least part of the fusion peptideis strongly correlated with activity whereas, γ-structure tends to beless prevalent, associated with non-native experimental conditions, and morerelated to vesicle aggregation than fusion. The specific angle of insertionof the peptides into the membrane plane is also found to be an importantcharacteristic for the fusion process. A shallow penetration, extending onlyto the central aliphatic core region, is likely responsible for the destabilization ofthe lipids required for coalescence of the apposing membranes and fusion.
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Röckendorf, Niels, Christian Nehls, and Thomas Gutsmann. "Design of Membrane Active Peptides Considering Multi-Objective Optimization for Biomedical Application." Membranes 12, no. 2 (February 2, 2022): 180. http://dx.doi.org/10.3390/membranes12020180.
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A multitude of membrane active peptides exists that divides into subclasses, such as cell penetrating peptides (CPPs) capable to enter eukaryotic cells or antimicrobial peptides (AMPs) able to interact with prokaryotic cell envelops. Peptide membrane interactions arise from unique sequence motifs of the peptides that account for particular physicochemical properties. Membrane active peptides are mainly cationic, often primary or secondary amphipathic, and they interact with membranes depending on the composition of the bilayer lipids. Sequences of these peptides consist of short 5–30 amino acid sections derived from natural proteins or synthetic sources. Membrane active peptides can be designed using computational methods or can be identified in screenings of combinatorial libraries. This review focuses on strategies that were successfully applied to the design and optimization of membrane active peptides with respect to the fact that diverse features of successful peptide candidates are prerequisites for biomedical application. Not only membrane activity but also degradation stability in biological environments, propensity to induce resistances, and advantageous toxicological properties are crucial parameters that have to be considered in attempts to design useful membrane active peptides. Reliable assay systems to access the different biological characteristics of numerous membrane active peptides are essential tools for multi-objective peptide optimization.
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Hamasaki, Naotaka, Hiroyuki Kuma, Kazuhisa Ota, Masao Sakaguchi, and Katsuyoshi Mihara. "A new concept in polytopic membrane proteins following from the study of band 3 protein." Biochemistry and Cell Biology 76, no. 5 (October 1, 1998): 729–33. http://dx.doi.org/10.1139/o98-085.
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In the present communication, we introduce a novel concept in multispanning polytopic membrane proteins revealed by the study of the band 3 protein. The transmembrane domain of such proteins can be divided into three categories, that is, hydrophilic loops connecting transmembrane peptides (category 1), portions embedded by peptide-peptide interactions (category 2), and portions embedded by peptide-lipid interactions (category 3). Category 2 peptides of polytopic membrane proteins were found to stably reside in the lipid bilayer without peptide-lipid interactions that had been thought to be essential for transmembrane segments. Category 3 peptides are equivalent to single-spanning segments of bitopic membrane proteins. Three different experiments, namely proteolytic digestion, chemical modification of the band 3 protein, and cell free transcription and translation, were used to categorize the transmembrane peptides.Key words: band 3 protein, transmembrane (TM) peptide, classification of TM, category 2-TM, polytopic membrane protein.
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Kondrashov, Oleg V., Peter I. Kuzmin, and Sergey A. Akimov. "Hydrophobic Mismatch Controls the Mode of Membrane-Mediated Interactions of Transmembrane Peptides." Membranes 12, no. 1 (January 13, 2022): 89. http://dx.doi.org/10.3390/membranes12010089.
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Various cellular processes require the concerted cooperative action of proteins. The possibility for such synchronization implies the occurrence of specific long-range interactions between the involved protein participants. Bilayer lipid membranes can mediate protein–protein interactions via relatively long-range elastic deformations induced by the incorporated proteins. We considered the interactions between transmembrane peptides mediated by elastic deformations using the framework of the theory of elasticity of lipid membranes. An effective peptide shape was assumed to be cylindrical, hourglass-like, or barrel-like. The interaction potentials were obtained for membranes of different thicknesses and elastic rigidities. Cylindrically shaped peptides manifest almost neutral average interactions—they attract each other at short distances and repel at large ones, independently of membrane thickness or rigidity. The hourglass-like peptides repel each other in thin bilayers and strongly attract each other in thicker bilayers. On the contrary, the barrel-like peptides repel each other in thick bilayers and attract each other in thinner membranes. These results potentially provide possible mechanisms of control for the mode of protein–protein interactions in membrane domains with different bilayer thicknesses.
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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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Bechinger, B., and S. U. Gorr. "Antimicrobial Peptides: Mechanisms of Action and Resistance." Journal of Dental Research 96, no. 3 (November 25, 2016): 254–60. http://dx.doi.org/10.1177/0022034516679973.
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More than 40 antimicrobial peptides and proteins (AMPs) are expressed in the oral cavity. These AMPs have been organized into 6 functional groups, 1 of which, cationic AMPs, has received extensive attention in recent years for their promise as potential antibiotics. The goal of this review is to describe recent advances in our understanding of the diverse mechanisms of action of cationic AMPs and the bacterial resistance against these peptides. The recently developed peptide GL13K is used as an example to illustrate many of the discussed concepts. Cationic AMPs typically exhibit an amphipathic conformation, which allows increased interaction with negatively charged bacterial membranes. Peptides undergo changes in conformation and aggregation state in the presence of membranes; conversely, lipid conformation and packing can adapt to the presence of peptides. As a consequence, a single peptide can act through several mechanisms depending on the peptide’s structure, the peptide:lipid ratio, and the properties of the lipid membrane. Accumulating evidence shows that in addition to acting at the cell membrane, AMPs may act on the cell wall, inhibit protein folding or enzyme activity, or act intracellularly. Therefore, once a peptide has reached the cell wall, cell membrane, or its internal target, the difference in mechanism of action on gram-negative and gram-positive bacteria may be less pronounced than formerly assumed. While AMPs should not cause widespread resistance due to their preferential attack on the cell membrane, in cases where specific protein targets are involved, the possibility exists for genetic mutations and bacterial resistance. Indeed, the potential clinical use of AMPs has raised the concern that resistance to therapeutic AMPs could be associated with resistance to endogenous host-defense peptides. Current evidence suggests that this is a rare event that can be overcome by subtle structural modifications of an AMP.
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Mirsaliotis, Antonis, Daniel Lamb, and David W. Brighty. "Nonhelical Leash and α-Helical Structures Determine the Potency of a Peptide Antagonist of Human T-Cell Leukemia Virus Entry." Journal of Virology 82, no. 10 (February 27, 2008): 4965–73. http://dx.doi.org/10.1128/jvi.02458-07.
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ABSTRACT Viral fusion proteins mediate the entry of enveloped viral particles into cells by inducing fusion of the viral and target cell membranes. Activated fusion proteins undergo a cascade of conformational transitions and ultimately resolve into a compact trimer of hairpins or six-helix bundle structure, which pulls the interacting membranes together to promote lipid mixing. Significantly, synthetic peptides based on a C-terminal region of the trimer of hairpins are potent inhibitors of membrane fusion and viral entry, and such peptides are typically extensively α-helical. In contrast, an atypical peptide inhibitor of human T-cell leukemia virus (HTLV) includes α-helical and nonhelical leash segments. We demonstrate that both the C helix and C-terminal leash are critical to the inhibitory activities of these peptides. Amino acid side chains in the leash and C helix extend into deep hydrophobic pockets at the membrane-proximal end of the HTLV type 1 (HTLV-1) coiled coil, and these contacts are necessary for potent antagonism of membrane fusion. In addition, a single amino acid substitution within the inhibitory peptide improves peptide interaction with the core coiled coil and yields a peptide with enhanced potency. We suggest that the deep pockets on the coiled coil are ideal targets for small-molecule inhibitors of HTLV-1 entry into cells. Moreover, the extended nature of the HTLV-1-inhibitory peptide suggests that such peptides may be intrinsically amenable to modifications designed to improve inhibitory activity. Finally, we propose that leash-like mimetic peptides may be of value as entry inhibitors for other clinically important viral infections.
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Martoglio, B. "Intramembrane proteolysis and post-targeting functions of signal peptides." Biochemical Society Transactions 31, no. 6 (December 1, 2003): 1243–47. http://dx.doi.org/10.1042/bst0311243.
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Signal sequences are the addresses of proteins destined for secretion. In eukaryotic cells, they mediate targeting to the endoplasmic reticulum membrane and insertion into the translocon. Thereafter, signal sequences are cleaved from the pre-protein and liberated into the endoplasmic reticulum membrane. We have recently reported that some liberated signal peptides are further processed by the intramembrane-cleaving aspartic protease signal peptide peptidase. Cleavage in the membrane-spanning portion of the signal peptide promotes the release of signal peptide fragments from the lipid bilayer. Typical processes that include intramembrane proteolysis is the regulatory or signalling function of cleavage products. Likewise, signal peptide fragments liberated upon intramembrane cleavage may promote such post-targeting functions in the cell.
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Clément, B., B. Segui-Real, P. Savagner, H. K. Kleinman, and Y. Yamada. "Hepatocyte attachment to laminin is mediated through multiple receptors." Journal of Cell Biology 110, no. 1 (January 1, 1990): 185–92. http://dx.doi.org/10.1083/jcb.110.1.185.
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The interaction of hepatocytes with the basement membrane glycoprotein laminin was studied using synthetic peptides derived from laminin sequences. Rat hepatocytes bind to laminin and three different sites within the A and B1 chains of laminin were identified. Active laminin peptides include the PA22-2 peptide (close to the carboxyl end of the long arm in the A chain), the RGD-containing peptide, PA21 (in the short arm of the A chain) and the pentapeptide YIGSR (in the short arm of the B1 chain). PA22-2 was the most potent peptide, whereas the other two peptides had somewhat lower activity. Furthermore, hepatocyte attachment to laminin was inhibited by the three peptides, with PA22-2 being the most active. Various proteins from isolated membranes of cell-surface iodinated hepatocytes bound to a laminin affinity column including three immunologically related binding proteins : Mr = 67,000, 45,000, and 32,000. Several proteins--Mr = 80,000, 55,000, and 38,000-36,000--with a lower affinity for laminin were also identified. Affinity chromatography on peptide columns revealed that the PA22-2 peptide specifically bound the Mr = 80,000, 67,000, 45,000, and 32,000 proteins, the PA21 peptide bound the Mr = 45,000 and 38,000-36,000 proteins and the YIGSR peptide column bound the 38,000-36,000 protein. Antisera to a bacterial fusion protein of the 32-kD laminin-binding protein (LBP-32) reacted strongly with the three laminin-binding proteins, Mr = 67,000, 45,000, and 32,000, showing that they are immunologically related. Immunoperoxidase microscopy studies confirmed that these proteins are present within the plasma membrane of the hepatocyte. The antisera inhibited the adhesion of hepatocytes to hepatocytes to laminin by 30%, supporting the finding that these receptors and others mediate the attachment of hepatocytes to several regions of laminin.
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SCHRAW, Todd D., Paula P. LEMONS, William L. DEAN, and Sidney W. WHITEHEART. "A role for Sec1/Munc18 proteins in platelet exocytosis." Biochemical Journal 374, no. 1 (August 15, 2003): 207–17. http://dx.doi.org/10.1042/bj20030610.
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A critical aspect of haemostasis is the release of clot-forming components from the three intra-platelet stores: dense-core granules, α granules and lysosomes. Exocytosis from these granules is mediated by soluble proteins [N-ethylmaleimide-sensitive fusion protein (NSF) and soluble NSF attachment proteins (SNAPs)] and integral membrane proteins [vesicle and target SNAP receptors (v- and t-SNAREs)]. Three Sec1/Munc18 proteins (SM proteins) are present in platelets (Munc18a, Munc18b and Munc18c) and they bind to and potentially regulate specific syntaxin t-SNAREs. In resting platelets, these SM proteins associate with granules and open canalicular system membranes predominantly but not with the plasma membrane. Munc18a binds to syntaxin 2 alone and does not associate with other members of the core SNARE complex. Munc18b associates with a larger complex that contains synaptosome-associated protein of 23 kDa (SNAP-23) and cellubrevin/vesicle-associated membrane protein 3. Munc18c associates with both syntaxins 2 and 4, with synaptosome-associated protein of 23 kDa (SNAP-23) and with a v-SNARE. On stimulation, most of the platelet SM proteins are still found in membrane fractions. Phosphorylation of each Munc18 increases in thrombin-treated cells and phosphorylated Munc18c remains associated with syntaxins 2 and 4, but its affinity for the SNAREs appears to be reduced. To determine the functional role of the platelet SM proteins, we examined the effects of Munc18-based peptides (Munc18a peptide 3 and Munc18c peptide 3). Addition of the peptides to permeabilized platelets inhibits secretion from all three platelet granules. These peptides also inhibit agonist-induced aggregation in saponin-permeabilized platelets. These studies demonstrate a clear role for SM proteins in platelet exocytosis and aggregation and suggest a dominant role for Munc18c in all three granule-release events.
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Ng, Sandy Y. M., David J. VanDyke, Bonnie Chaban, John Wu, Yoshika Nosaka, Shin-Ichi Aizawa, and Ken F. Jarrell. "Different Minimal Signal Peptide Lengths Recognized by the Archaeal Prepilin-Like Peptidases FlaK and PibD." Journal of Bacteriology 191, no. 21 (August 28, 2008): 6732–40. http://dx.doi.org/10.1128/jb.00673-09.
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ABSTRACT In Archaea, the preflagellin peptidase (a type IV prepilin-like peptidase designated FlaK in Methanococcus voltae and Methanococcus maripaludis) is the enzyme that cleaves the N-terminal signal peptide from preflagellins. In methanogens and several other archaeal species, the typical flagellin signal peptide length is 11 to 12 amino acids, while in other archaea preflagellins possess extremely short signal peptides. A systematic approach to address the signal peptide length requirement for preflagellin processing is presented in this study. M. voltae preflagellin FlaB2 proteins with signal peptides 3 to 12 amino acids in length were generated and used as a substrate in an in vitro assay utilizing M. voltae membranes as an enzyme source. Processing by FlaK was observed in FlaB2 proteins containing signal peptides shortened to 5 amino acids; signal peptides 4 or 3 amino acids in length were unprocessed. In the case of Sulfolobus solfataricus, where the preflagellin peptidase PibD has broader substrate specificity, some predicted substrates have predicted signal peptides as short as 3 amino acids. Interestingly, the shorter signal peptides of the various mutant FlaB2 proteins not processed by FlaK were processed by PibD, suggesting that some archaeal preflagellin peptidases are likely adapted toward cleaving shorter signal peptides. The functional complementation of signal peptidase activity by FlaK and PibD in an M. maripaludis ΔflaK mutant indicated that processing of preflagellins was detected by complementation with either FlaK or PibD, yet only FlaK-complemented cells were flagellated. This suggested that a block in an assembly step subsequent to signal peptide removal occurred in the PibD complementation.
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Shmulevitz, Maya, Raquel F. Epand, Richard M. Epand, and Roy Duncan. "Structural and Functional Properties of an Unusual Internal Fusion Peptide in a Nonenveloped Virus Membrane Fusion Protein." Journal of Virology 78, no. 6 (March 15, 2004): 2808–18. http://dx.doi.org/10.1128/jvi.78.6.2808-2818.2004.
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ABSTRACT The avian and Nelson Bay reoviruses are two of only a limited number of nonenveloped viruses capable of inducing cell-cell membrane fusion. These viruses encode the smallest known membrane fusion proteins (p10). We now show that a region of moderate hydrophobicity we call the hydrophobic patch (HP), present in the small N-terminal ectodomain of p10, shares the following characteristics with the fusion peptides of enveloped virus fusion proteins: (i) an abundance of glycine and alanine residues, (ii) a potential amphipathic secondary structure, (iii) membrane-seeking characteristics that correspond to the degree of hydrophobicity, and (iv) the ability to induce lipid mixing in a liposome fusion assay. The p10 HP is therefore predicted to provide a function in the mechanism of membrane fusion similar to those of the fusion peptides of enveloped virus fusion peptides, namely, association with and destabilization of opposing lipid bilayers. Mutational and biophysical analysis suggested that the internal fusion peptide of p10 lacks alpha-helical content and exists as a disulfide-stabilized loop structure. Similar kinked structures have been reported in the fusion peptides of several enveloped virus fusion proteins. The preservation of a predicted loop structure in the fusion peptide of this unusual nonenveloped virus membrane fusion protein supports an imperative role for a kinked fusion peptide motif in biological membrane fusion.
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Eissa, N. G., E. J. Sayers, D. Birch, S. G. Patel, Y. H. Tsai, H. Mørck Nielsen, and A. T. Jones. "EJP18 peptide derived from the juxtamembrane domain of epidermal growth factor receptor represents a novel membrane-active cell-penetrating peptide." Biochemical Journal 477, no. 1 (January 8, 2020): 45–60. http://dx.doi.org/10.1042/bcj20190452.
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Membrane-active peptides have been extensively studied to probe protein–membrane interactions, to act as antimicrobial agents and cell-penetrating peptides (CPPs) for the delivery of therapeutic agents to cells. Hundreds of membrane-active sequences acting as CPPs have now been described including bioportides that serve as single entity modifiers of cell physiology at the intracellular level. Translation of promising CPPs in pre-clinical studies have, however, been disappointing as only few identified delivery systems have progressed to clinical trials. To search for novel membrane-active peptides a sequence from the EGFR juxtamembrane region was identified (named EJP18), synthesised, and examined in its L- and D-form for its ability to mediate the delivery of a small fluorophore and whole proteins to cancer cell lines. Initial studies identified the peptide as being highly membrane-active causing extensive and rapid plasma membrane reorganisation, blebbing, and toxicity. At lower, non-toxic concentrations the peptides outperformed the well-characterised CPP octaarginine in cellular delivery capacity for a fluorophore or proteins that were associated with the peptide covalently or via ionic interactions. EJP18 thus represents a novel membrane-active peptide that may be used as a naturally derived model for biophysical protein–membrane interactions or for delivery of cargo into cells for therapeutic or diagnostic applications.
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Skehel, J. J., K. Cross, D. Steinhauer, and D. C. Wiley. "Influenza fusion peptides." Biochemical Society Transactions 29, no. 4 (August 1, 2001): 623–26. http://dx.doi.org/10.1042/bst0290623.
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The ‘fusion peptides’ of a group of enveloped viruses that includes influenza, paramyxo-, retro-and filo-viruses are N-terminal regions of their membrane fusion proteins generated by cleavage of non-functional precursors. For the influenza membrane fusion protein, haemagglutinin (HA), the three-dimensional structures of precursor HA, cleaved HA and fusion-activated HA show that the fusion peptides are located in different positions in all three forms and adopt different structures. Analyses of mutant HAs with changes in fusion peptide sequence indicate the importance of specific residues for membrane-fusion activity and suggest a structure for the fusion peptide in a fusion-active molecule.
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Dahiya, Sunita, and Rajiv Dahiya. "BIOAVAILABILITY ENHANCEMENT AND LIPID NANOCARRIER BASED DELIVERY OF PEPTIDES AND PROTEINS." Bulletin of Pharmaceutical Research 10, no. 1-3 (2020): 1–10. http://dx.doi.org/10.21276/bpr.2020.10.3.
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Peptides and proteins are vital biomacromolecules that perform several bodily functions in various physiological and biological processes. Being biocompatible and biodegradable, these macromolecules are considered promising platforms for delivery of drugs and genes. However, peptides and proteins suffer from major limitations including enzymatic degradation, short circulation half-lives, and poor membrane permeability that leads to poor bioavailability, challenging their effective delivery. This article briefly discusses the inherent challenges in peptide and protein delivery along with strategies for bioavailability enhancement and lipid nanocarriers as prospective systems for peptide and protein drug delivery.
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Marsh, D. "Application of electron spin resonance for investigating peptide-lipid interactions, and correlation with thermodynamics." Biochemical Society Transactions 29, no. 4 (August 1, 2001): 582–89. http://dx.doi.org/10.1042/bst0290582.
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Peptide-lipid interactions can be investigated with spin-labelled lipid probes by using electron spin resonance (ESR) methods that have been developed for studying lipid-protein interactions with both integral and peripheral membrane proteins and also with surface-binding proteins that additionally penetrate the membrane. This approach has the advantage that a direct comparison can be made with the databank of ESR results from the various types of membrane protein. The appropriateness of the peptides as models for membrane proteins, or for their specific segments, can then be assessed. Further, differences in behaviour can be readily identified, as for example in the case of surface-active cytolytic or fusogenic peptides. Comparison with thermodynamic predictions for membrane insertion provides a useful adjunct to the spin-label method.
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Żyłka, Romuald, Justyna Kupiec, and Stanislaw Przestalski. "Peptides conformational changes of the erythrocyte membrane induced by organometallic tin compounds." Current Topics in Biophysics 34, no. 1 (January 1, 2011): 31–35. http://dx.doi.org/10.2478/v10214-011-0005-2.
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Peptides conformational changes of the erythrocyte membrane induced by organometallic tin compoundsThe paper presents the results of a study on the effect of selected organic chlorides of tin on peptide conformations of erythrocyte ghosts from pig blood. The following compounds were used: dibutyltin dichloride (DBT), tributyltin chloride (TBT), diphenyltin dichloride (DPhT) and triphenyltin chloride (TPhT). Peptide conformation changes were determined on the basis of measurements done with the ATR FTIR technique. This method made it possible to measure the percent share of a peptide with specified conformation in the whole amount of the peptides in the membranes studied. The investigation showed that all the tin organic compounds studied cause a several-percent decrease in the quantities of both the peptides with the α-helix and turn conformation, and about a 20% increase in ghost peptides with β-sheet conformation. It seems that the changes observed can cause disturbances in the function of proteins and, consequently, the activity of the membrane; and this may be one of the aspects of the toxic properties of organotins.
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Szachowicz-Petelska, Barbara, Stanisław Sulkowski, and Zbigniew Figaszewski. "Altered membrane amino acids composition in human colorectal cancer tissue." Open Chemistry 10, no. 4 (August 1, 2012): 1245–52. http://dx.doi.org/10.2478/s11532-012-0050-1.
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AbstractCancer transformation is characterized by changes in cell metabolism, which can alter the structure and function of cell membrane components, including integral membrane proteins. Qualitative and quantitative estimations of integral membrane protein are necessary for studies aimed at understanding their modifications under pathological conditions. Herein, we used a high-performance liquid chromatography (HPLC)-based approach that involved selective hydrolysis of isolated tissue cell membrane proteins to peptides, resolution by chromatography and determination of the amino acid content (phenylalanine (Phe), tyrosine (Tyr), cysteine (Cys) and lysine (Lys)) in individual peptides. The results demonstrate decrease in peptide levels and their amino acids content in integral membrane proteins in human colorectal cancer tissue. Therefore, cancer transformation causes a decrease in the levels of integral membrane proteins, which may in turn lead to an increase in the levels of other charged molecules on the cell surface, such as phospholipids. It might lead to the reconstruction and functional rearrangement of the cell membrane, for example: the permeability, electric properties, fluidity etc.
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Reinhardt, Timothy A., and John D. Lippolis. "Bovine Milk Fat Globule Membrane Proteome." Journal of Dairy Research 73, no. 4 (July 12, 2006): 406–16. http://dx.doi.org/10.1017/s0022029906001889.
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Milk fat globule membranes (MFGM) were isolated from the milk of mid-lactation Holstein cows. The purified MFGM were fractionated using 1-dimensional SDS gels. Tryptic peptides from gel slices were further fractionated on a micro-capillary high performance liquid chromatograph connected to a nanospray-tandem mass spectrometer. Analysis of the data resulted in 120 proteins being identified by two or more unique peptide sequences. Of these 120 proteins, 71% are membrane associated proteins with the remainder being cytoplasmic or secreted proteins. Only 15 of the proteins identified in the cow MFGM were the same as proteins identified in previous mouse or human MFGM proteomic studies. Thus, the bulk of the proteins identified are new for bovine MFGM proteomics. The proteins identified were associated with membrane/protein trafficking (23%), cell signalling (23%), unknown functions (21%), fat transport/metabolism (11%), transport (9%), protein synthesis/folding (7%), immune proteins (4%) and milk proteins (2%). The proteins associated with cell signalling or membrane/protein trafficking may provide insights into MFGM secretion mechanisms. The finding of CD14, toll like receptor (TLR2), and TLR4 on MFGM suggests a direct role for the mammary gland in detecting an infection.
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Wang, Guangshun. "NMR of Membrane-Associated Peptides and Proteins." Current Protein & Peptide Science 9, no. 1 (February 1, 2008): 50–69. http://dx.doi.org/10.2174/138920308783565714.
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Clague, M. J., and R. J. Cherry. "Comparison of p25 presequence peptide and melittin. Red blood cell haemolysis and band 3 aggregation." Biochemical Journal 252, no. 3 (June 15, 1988): 791–94. http://dx.doi.org/10.1042/bj2520791.
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The 25 residue presequence (p25) for subunit IV of yeast cytochrome oxidase had previously been shown to possess structural and behavioural characteristics in common with the bee venom polypeptide, melittin. The present study extends the results of leakage experiments on model-membrane systems to the haemolysis of human erythrocytes, which both peptides are shown to accomplish in a manner sensitive to membrane potential. In addition, the laser flash-induced transient dichroism technique for measuring protein rotational diffusion has been used to show that both peptides aggregate band 3, the major integral membrane protein of the erythrocyte. Aggregation cannot be reversed by high ionic strength; this serves to differentiate these peptides from other positively charged species such as polylysine that aggregate band 3 at low ionic strength. These results suggest that aggregation of membrane proteins may possibly prove to be a feature of the interaction of p25 signal peptide with mitochondrial membranes.
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Wang, P., G. Gyllner, and S. Kvist. "Selection and binding of peptides to human transporters associated with antigen processing and rat cim-a and -b." Journal of Immunology 157, no. 1 (July 1, 1996): 213–20. http://dx.doi.org/10.4049/jimmunol.157.1.213.
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Abstract Cytotoxic T lymphocytes recognize antigenic peptides presented by MHC class I molecules. The peptides are generated in the cytosol by proteasomes, and probably also other proteases, and are then translocated into the endoplasmic reticulum (ER) lumen. The transporters associated with Ag processing (TAP) are key molecules for transporting peptides from the cytosol to the lumen of the ER. Using semipermeabilized cells, TAP-dependent peptide translocation was demonstrated, and the selectivity of peptide translocation was based on the carboxyl-terminal amino acid of peptides. We have examined peptide binding proteins in the ER membrane and the selection of peptides for binding to TAP by using a panel of peptides of different sequences and carboxyl-termini as well as peptides containing D amino acids. Peptides bound to TAP molecules in the absence of ATP. The presence of ATP induced binding of peptides to two additional membrane proteins (58 and 43 kDa). The selection of peptides by TAP molecules was based on peptide sequence and the carboxyl-terminal amino acid. Peptides containing D amino acid did not bind to TAP molecules. Rat cim-a and -b selected peptides differently, and selection was not only dependent on the carboxyl-terminal residue of the peptide, but included an influence of the peptide sequence. The different off-rates after peptide binding to TAP, indicated a dual binding step of peptide to TAP. ATP regulated the off-rate of peptides at a high affinity binding step. Our results demonstrate that the binding of peptides to TAP molecules is specific and most likely involves a multiple step pathway.
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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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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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Hiken, Jeffrey, Richard LeDuc, Petra Gilmore, Henry Rohrs, R. Reid Townsend, and Monica Bessler. "Global Differences in RBC Membrane Protein Expression Between Normal and PNH Individuals." Blood 114, no. 22 (November 20, 2009): 1986. http://dx.doi.org/10.1182/blood.v114.22.1986.1986.
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Abstract Abstract 1986 Poster Board I-1008 Paroxysmal nocturnal hemoglobinuria (PNH) is an acquired hemolytic anemia that results from the deficiency of glycosyl phosphatidylinositol (GPI)-linked proteins on the surface of blood cells carrying a PIGA gene mutation. The absence of 2 GPI-linked complement regulatory proteins, CD59 and CD55, on PNH red blood cells (RBCs) accounts for their increased susceptibility to complement-mediated lysis. The pathophysiology of other PNH complications, including thrombophilia and the association with aplastic anemia, is less well understood. We hypothesized that the differences between PNH and normal RBCs are not restricted to the lack of GPI-linked proteins. To test this hypothesis we have developed a label-free proteomics platform to identify global differences in RBC membrane protein expression between normal and PNH individuals. Six control samples and 17 PNH samples from 13 different patients were analyzed. PNH patients were categorized as high (>80%), medium (between 20% and 80%), and low (<20%), based on their combined percentage of type II and type III PNH RBCs. RBC membranes were prepared, and proteins were extracted and subjected to trypsin digest. Peptides were then analysed by nano-liquid chromatography coupled to tandem mass spectrometry (nanoLC-MS/MS). All 23 nanoLC-MS/MS runs (6 control and 17 PNH) were aligned, and peptide ion currents were extracted and normalized for relative quantitation of peptide abundances and inference of relative protein abundance. ANOVA analyses of the different sample classes were performed in order to distinguish differences in the relative abundances at the peptide level (from a dataset containing ∼30,000 peptides). Comparison of control vs. high PNH samples yielded a set of 142 peptides showing patterns of expression that clearly separated the two groups. Targeted nanoLC-MS/MS identified the differential expression of peptides from 5 of the 8 known GPI-linked proteins expressed on human RBCs. As expected, the relative abundances of these peptides were inversely related to the percentage of PNH RBCs in the samples. In addition, we found peptides from complement protein C3 increased on PNH RBCs from patients receiving the complement C5 inhibitor eculizumab. We have developed a statistical model that uses peptide ion intensities to infer relative abundance at the protein level, and allows for significance testing between healthy and disease groups. RBC membranes from the 6 normal control and 7 high PNH samples were processed using MS with ‘data-dependant acquisition', which is biased towards annotation of the more abundant peptides. 1676 peptides from 119 proteins were annotated with high confidence. Nine of these showed a significant difference between control and PNH, including CD59 and semaphorin-7A, the 2 known GPI-linked proteins annotated in this experiment. The remaining 7 non-GPI-linked proteins were peroxiredoxin-2 (PXDN2), valosin-containing protein, gamma-actin, catalase (CATA), heat shock protein 90A, flotilin-1, and RAP1A. Several of these non-GPI-linked proteins are of potential interest to the PNH phenotype or PNH pathophysiology. The anti-oxidative enzymes CATA and PXDN2 both showed significantly lower levels associated with PNH RBC membranes compared to control, and may contribute to an increased susceptibility of the PNH RBC plasma membrane to oxidative damage. The small G-protein RAP1A showed a significantly elevated expression in PNH RBC membrane preparations. RAP1A activation mediates increased sickle cell RBC adhesion to laminin (Blood, 105: 3322), suggesting that elevated RAP1A levels may also contribute to the increased propensity of thrombosis in PNH patients. In summary, differential protein expression analysis indicates that PNH and normal RBCs differ by more than only the lack of GPI-linked proteins. Differences in protein expression are likely to contribute to disease manifestations and are likely to provide insights into additional unexpected underlying disease processes. Future studies will investigate longitudinal changes in the RBC proteome during the course of the disease and in response to treatment, potentially providing new biomarkers that help to distinguish patients at risk for complications and patients likely to benefit from specific forms of treatment. Our comparative label-free proteomics platform should be broadly applicable to the analysis of other RBC disorders. Disclosures: Bessler: Alexion Pharaceuticals Inc: Membership on an entity's Board of Directors or advisory committees.
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Shai, Yechiel. "Functional Domains within Fusion Proteins: Prospectives for Development of Peptide Inhibitors of Viral Cell Fusion." Bioscience Reports 20, no. 6 (December 1, 2000): 535–55. http://dx.doi.org/10.1023/a:1010411021326.
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The entry of enveloped viruses into host cells is accomplished by fusion ofthe viral envelope and target plasma membrane and is mediated by fusionproteins. Recently, several functional domains within fusion proteins fromdifferent viral families were identified. Some are directly involved inconformational changes after receptor binding, as suggested by the recentrelease of crystallographically determined structures of a highly stablecore structure of the fusion proteins in the absence of membranes. However, in the presence of membranes, this core binds strongly to the membrane's surface and dissociates therein. Other regions, besides the N-terminal fusionpeptide, which include the core region and an internal fusion peptide inparamyxoviruses, are directly involved in the actual membrane fusion event, suggesting an “umbrella” like model for the membrane inducedconformational change of fusion proteins. Peptides resembling these regionshave been shown to have specific antiviral activity, presumably because theyinterfere with the corresponding domains within the viruses. Overall, thesestudies shed light into the molecular mechanism of membrane fusion induced byenvelope glycoproteins and suggest that fusion proteins from different viralfamilies share common structural and functional motifs.
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Jeong, Sekyoo, Seokjeong Yoon, Sungwoo Kim, Juyeon Jung, Myungho Kor, Kayoung Shin, Chaejin Lim, et al. "Anti-Wrinkle Benefits of Peptides Complex Stimulating Skin Basement Membrane Proteins Expression." International Journal of Molecular Sciences 21, no. 1 (December 20, 2019): 73. http://dx.doi.org/10.3390/ijms21010073.
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The dermal-epidermal junction (DEJ) provides a physical and biological interface between the epidermis and the dermis. In addition to providing a structural integrity, the DEJ also acts as a passageway for molecular transport. Based on the recently reported importance of the DEJ in skin aging, novel peptide derivatives have been tested for their effects on basement membrane (BM) protein expressions in cultured human epidermal keratinocytes. As a result, protein expressions of collagen XVII, laminin and nidogen were stimulated by the test peptide and peptides complex. Further ex vivo evaluation using excised human skin, confirmed that the topical application of the peptides complex significantly increased dermal collagen expression, as well as expressions of collagen XVII and laminin. Interestingly, while the origin of the laminin protein is epidermal keratinocytes, the immunohistochemical staining of skin showed that laminin was only detected in the uppermost layer of the dermis, which suggests a tight assembly of laminin protein onto the dermal side of the DEJ. These results suggest that a peptide complex could improve the structural properties of the DEJ through its ability to stimulate BM proteins. In order to evaluate the anti-wrinkle benefits of the peptide complex in vivo, a clinical study was performed on 22 healthy Asian female volunteers older than 40 years. As a result, significant improvements in skin wrinkles for all of the five sites were observed after two weeks, as assessed by skin topographic measurements. Collectively, these results demonstrate the anti-aging efficacy of the peptides complex.
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Lear, J. D., H. Gratkowski, and W. F. DeGrado. "De novo design, synthesis and characterization of membrane-active peptides." Biochemical Society Transactions 29, no. 4 (August 1, 2001): 559–64. http://dx.doi.org/10.1042/bst0290559.
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Our current level of understanding of membrane-protein folding is primitive, but it is beginning to advance. Previously [Choma, Gratkowski, Lear and DeGrado (2000) Nat. Struct. Biol. 7, 161–166], we described studies of the association in detergent micelles of short, simple-sequence hydrophobic peptides modified from the sequence of the water-soluble, homodimeric coiled-coil GCN4-P1 peptide using the principle that the interiors of membrane proteins are similar to those of water-soluble proteins. Here, we discuss more quantitative aspects of the association equilibrium and compare the free energies of association of a number of mutant peptides designed to explore specific features responsible for the association.
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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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Lee, Ernest Y., Benjamin M. Fulan, Gerard C. L. Wong, and Andrew L. Ferguson. "Mapping membrane activity in undiscovered peptide sequence space using machine learning." Proceedings of the National Academy of Sciences 113, no. 48 (November 14, 2016): 13588–93. http://dx.doi.org/10.1073/pnas.1609893113.
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There are some ∼1,100 known antimicrobial peptides (AMPs), which permeabilize microbial membranes but have diverse sequences. Here, we develop a support vector machine (SVM)-based classifier to investigate ⍺-helical AMPs and the interrelated nature of their functional commonality and sequence homology. SVM is used to search the undiscovered peptide sequence space and identify Pareto-optimal candidates that simultaneously maximize the distanceσfrom the SVM hyperplane (thus maximize its “antimicrobialness”) and its ⍺-helicity, but minimize mutational distance to known AMPs. By calibrating SVM machine learning results with killing assays and small-angle X-ray scattering (SAXS), we find that the SVM metricσcorrelates not with a peptide’s minimum inhibitory concentration (MIC), but rather its ability to generate negative Gaussian membrane curvature. This surprising result provides a topological basis for membrane activity common to AMPs. Moreover, we highlight an important distinction between the maximal recognizability of a sequence to a trained AMP classifier (its ability to generate membrane curvature) and its maximal antimicrobial efficacy. As mutational distances are increased from known AMPs, we find AMP-like sequences that are increasingly difficult for nature to discover via simple mutation. Using the sequence map as a discovery tool, we find a unexpectedly diverse taxonomy of sequences that are just as membrane-active as known AMPs, but with a broad range of primary functions distinct from AMP functions, including endogenous neuropeptides, viral fusion proteins, topogenic peptides, and amyloids. The SVM classifier is useful as a general detector of membrane activity in peptide sequences.
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Braunagel, Julia, Ann Junghans, and Ingo Köper. "Membrane-Based Sensing Approaches." Australian Journal of Chemistry 64, no. 1 (2011): 54. http://dx.doi.org/10.1071/ch10347.
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Tethered bilayer lipid membranes can be used as model platforms to host membrane proteins or membrane-active peptides, which can act as transducers in sensing applications. Here we present the synthesis and characterization of a valinomycin derivative, a depsipeptide that has been functionalized to serve as a redox probe in a lipid bilayer. In addition, we discuss the influence of the molecular structure of the lipid bilayer on its ability to host proteins. By using electrical impedance techniques as well as neutron scattering experiments, a clear correlation between the packing density of the lipids forming the membrane and its ability to host membrane proteins could be shown.
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Siminovitch, David J. "Solid-state NMR studies of proteins: the view from static 2H NMR experiments." Biochemistry and Cell Biology 76, no. 2-3 (May 1, 1998): 411–22. http://dx.doi.org/10.1139/o98-054.
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The application of solid-state 2H NMR spectroscopy to the study of protein and peptide structure and dynamics is reviewed. The advantages of solid-state NMR for the study of proteins are considered, and the particular advantages of solid-state 2H NMR are summarized. Examples of work on the integral membrane protein bacteriorhodopsin, and the membrane peptide gramicidin, are used to highlight the major achievements of the 2H NMR technique. These examples demonstrate that through the use of oriented samples, it is possible to obtain both structural and dynamic information simultaneously.Key words: solid-state NMR, 2H NMR, membrane peptides, membrane proteins, oriented bilayers.
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Chicz, R. M., D. F. Graziano, M. Trucco, J. L. Strominger, and J. C. Gorga. "HLA-DP2: self peptide sequences and binding properties." Journal of Immunology 159, no. 10 (November 15, 1997): 4935–42. http://dx.doi.org/10.4049/jimmunol.159.10.4935.
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Abstract Although self peptides bound to HLA-DQ and, especially, HLA-DR allotypes have been described in some detail, few ligands that bind to HLA-DP have been identified. Toward this aim, naturally processed peptides were isolated from immunoaffinity-purified HLA-DP2 molecules expressed in cultured B lymphocytes. The size distribution of the peptide repertoire is generally similar to those reported for self peptides bound to HLA-DR and HLA-DQ molecules. Twelve peptides representing individual sequences including two nested sets were sequenced by mass spectrometry and/or N-terminal Edman analysis. Source proteins included MHC molecules and other integral membrane proteins as well as secretory and serum proteins. No dominant amino acid markers suggestive of particular enzymatic processing events were detected. Peptide specificity and affinity were examined in binding assays using synthetic peptides and purified HLA-DP and HLA-DR molecules. Anchor residues were tentatively assigned using alanine-substituted analogues of two self peptides. Some structural features of HLA-DP2 that may relate to peptide binding are considered.
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Liu, Betty Revon, Shiow-Her Chiou, Yue-Wern Huang, and Han-Jung Lee. "Bio-Membrane Internalization Mechanisms of Arginine-Rich Cell-Penetrating Peptides in Various Species." Membranes 12, no. 1 (January 13, 2022): 88. http://dx.doi.org/10.3390/membranes12010088.
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Recently, membrane-active peptides or proteins that include antimicrobial peptides (AMPs), cytolytic proteins, and cell-penetrating peptides (CPPs) have attracted attention due to their potential applications in the biomedical field. Among them, CPPs have been regarded as a potent drug/molecules delivery system. Various cargoes, such as DNAs, RNAs, bioactive proteins/peptides, nanoparticles and drugs, can be carried by CPPs and delivered into cells in either covalent or noncovalent manners. Here, we focused on four arginine-rich CPPs and reviewed the mechanisms that these CPPs used for intracellular uptake across cellular plasma membranes. The varying transduction efficiencies of them alone or with cargoes were discussed, and the membrane permeability was also expounded for CPP/cargoes delivery in various species. Direct membrane translocation (penetration) and endocytosis are two principal mechanisms for arginine-rich CPPs mediated cargo delivery. Furthermore, the amino acid sequence is the primary key factor that determines the cellular internalization mechanism. Importantly, the non-cytotoxic nature and the wide applicability make CPPs a trending tool for cellular delivery.
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Porotto, Matteo, Christine C. Yokoyama, Laura M. Palermo, Bruce Mungall, Mohamad Aljofan, Riccardo Cortese, Antonello Pessi, and Anne Moscona. "Viral Entry Inhibitors Targeted to the Membrane Site of Action." Journal of Virology 84, no. 13 (March 31, 2010): 6760–68. http://dx.doi.org/10.1128/jvi.00135-10.
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ABSTRACT The fusion of enveloped viruses with the host cell is driven by specialized fusion proteins to initiate infection. The “class I” fusion proteins harbor two regions, typically two heptad repeat (HR) domains, which are central to the complex conformational changes leading to fusion: the first heptad repeat (HRN) is adjacent to the fusion peptide, while the second (HRC) immediately precedes the transmembrane domain. Peptides derived from the HR regions can inhibit fusion, and one HR peptide, T20 (enfuvirtide), is in clinical use for HIV-1. For paramyxoviruses, the activities of two membrane proteins, the receptor-binding protein (hemagglutinin-neuraminidase [HN] or G) and the fusion protein (F), initiate viral entry. The binding of HN or G to its receptor on a target cell triggers the activation of F, which then inserts into the target cell and mediates the membrane fusion that initiates infection. We have shown that for paramyxoviruses, the inhibitory efficacy of HR peptides is inversely proportional to the rate of F activation. For HIV-1, the antiviral potency of an HRC-derived peptide can be dramatically increased by targeting it to the membrane microdomains where fusion occurs, via the addition of a cholesterol group. We report here that for three paramyxoviruses—human parainfluenza virus type 3 (HPIV3), a major cause of lower respiratory tract diseases in infants, and the emerging zoonotic viruses Hendra virus (HeV) and Nipah virus (NiV), which cause lethal central nervous system diseases—the addition of cholesterol to a paramyxovirus HRC-derived peptide increased antiviral potency by 2 log units. Our data suggest that this enhanced activity is indeed the result of the targeting of the peptide to the plasma membrane, where fusion occurs. The cholesterol-tagged peptides on the cell surface create a protective antiviral shield, target the F protein directly at its site of action, and expand the potential utility of inhibitory peptides for paramyxoviruses.
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Lee, Jung-Seok, Goran Mitulović, Layla Panahipour, and Reinhard Gruber. "Proteomic Analysis of Porcine-Derived Collagen Membrane and Matrix." Materials 13, no. 22 (November 17, 2020): 5187. http://dx.doi.org/10.3390/ma13225187.
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Collagen membranes and matrices being widely used in guided bone regeneration and soft tissue augmentation have characteristic properties based on their composition. The respective proteomic signatures have not been identified. Here, we performed a high-resolution shotgun proteomic analysis on two porcine collagen-based biomaterials designed for guided bone regeneration and soft tissue augmentation. Three lots each of a porcine-derived collagen membrane and a matrix derived from peritoneum and/or skin were digested and separated by nano-reverse-phase high-performance liquid chromatography. The peptides were subjected to mass spectrometric detection and analysis. A total of 37 proteins identified by two peptides were present in all collagen membranes and matrices, with 11 and 16 proteins being exclusively present in the membrane and matrix, respectively. The common extracellular matrix proteins include fibrillar collagens (COL1A1, COL1A2, COL2A1, COL3A1, COL5A1, COL5A2, COL5A3, COL11A2), non-fibrillar collagens (COL4A2, COL6A1, COL6A2, COL6A3, COL7A1, COL16A1, COL22A1), and leucine-rich repeat proteoglycans (DCN, LUM, BGN, PRELP, OGN). The structural proteins vimentin, actin-based microfilaments (ACTB), annexins (ANXA1, ANXA5), tubulins (TUBA1B, TUBB), and histones (H2A, H2B, H4) were also identified. Examples of membrane-only proteins are COL12A1 and COL14A1, and, of matrix only proteins, elastin (ELN). The proteomic signature thus revealed the similarities between but also some individual proteins of collagen membrane and matrix.
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Volynsky, P. E., T. R. Galimzyanov, and S. A. Akimov. "Interaction of Peptides Containing CRAC Motifs with Lipids in Membranes of Various Composition." Biochemistry (Moscow), Supplement Series A: Membrane and Cell Biology 15, no. 2 (April 2021): 120–29. http://dx.doi.org/10.1134/s1990747821010074.
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Abstract The lateral distribution of integral and peripheral proteins, as well as lipids in the plasma membranes of mammalian cells is extremely heterogeneous. It is believed that various lipid-protein domains are formed in membranes. Domains enriched in sphingomyelin and cholesterol are called rafts. It is assumed that the distribution of proteins into rafts is largely related to the presence in their primary sequence of a specific amino acid region called the CRAC motif, which is responsible for cholesterol binding. In this work, the interaction of two peptides containing CRAC motifs in their structure with membranes of different compositions was studied by means of molecular dynamics. It has been shown that the average number of lipid molecules in contact with each peptide is proportional to the mole fraction of lipid in the membrane. The predominant interaction of peptides with cholesterol was not observed. In addition, cholesterol did not form long-lived contacts with any amino acid or amino acid sequence. We suppose that in some cases the predominant lateral distribution of peptides and proteins containing CRAC motifs into rafts may be due to amphipathicity of the CRAC motif rather than due to specific strong binding of cholesterol.
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Müller, W. E., C. Kirsch, and G. P. Eckert. "Membrane-disordering effects of β-amyloid peptides." Biochemical Society Transactions 29, no. 4 (August 1, 2001): 617–23. http://dx.doi.org/10.1042/bst0290617.
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β-Amyloid (Aβ) protein is the major constituent of senile plaques and cerebrovascular deposits characteristic of Alzheimer's disease (AD). The causal relationship between Aβ and AD-specific lesions like neurodegeneration and atrophy is still not known. The present article summarizes our studies indicating that rather low concentrations of Aβ significantly alter the fluidity of cell membranes and subcellular fractions from different tissues and different species including humans, as a possible initial step of its biological effects. Using different fluorescent probes our data show clearly that Aβ peptides specifically disturb the acylchain layer of cell membranes in a very distinct fashion. By contrast, membrane properties at the level of the polar heads of the phospholipid bilayer at the interface with membrane proteins are much less affected.
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Tao, Houchao, Sung Chang Lee, Arne Moeller, Rituparna Sinha Roy, Fai Yiu Siu, Jörg Zimmermann, Raymond C. Stevens, Clinton S. Potter, Bridget Carragher, and Qinghai Zhang. "Engineered nanostructured β-sheet peptides protect membrane proteins." Nature Methods 10, no. 8 (June 30, 2013): 759–61. http://dx.doi.org/10.1038/nmeth.2533.
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Wenzel, M., A. I. Chiriac, A. Otto, D. Zweytick, C. May, C. Schumacher, R. Gust, et al. "Small cationic antimicrobial peptides delocalize peripheral membrane proteins." Proceedings of the National Academy of Sciences 111, no. 14 (March 24, 2014): E1409—E1418. http://dx.doi.org/10.1073/pnas.1319900111.
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Killian, J. Antoinette. "Synthetic peptides as models for intrinsic membrane proteins." FEBS Letters 555, no. 1 (October 15, 2003): 134–38. http://dx.doi.org/10.1016/s0014-5793(03)01154-2.
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Kuchler, K., and J. Thorner. "Membrane translocation of proteins without hydrophobic signal peptides." Current Opinion in Cell Biology 2, no. 4 (August 1990): 617–24. http://dx.doi.org/10.1016/0955-0674(90)90102-k.
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Makkar, Sarbjeet, Rohana Liyanage, Lakshmi Kannan, Balamurugan Packialakshmi, Jack O. Lay, and Narayan C. Rath. "Chicken Egg Shell Membrane Associated Proteins and Peptides." Journal of Agricultural and Food Chemistry 63, no. 44 (October 28, 2015): 9888–98. http://dx.doi.org/10.1021/acs.jafc.5b04266.
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Takano, Mikihisa, and Yumoto Ryoko. "Transport of Proteins and Peptides and its Regulation in Alveolar Epithelial Cells." MEMBRANE 36, no. 4 (2011): 145–53. http://dx.doi.org/10.5360/membrane.36.145.
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Epand, Richard M. "Membrane Fusion." Bioscience Reports 20, no. 6 (December 1, 2000): 435–41. http://dx.doi.org/10.1023/a:1010498618600.
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The fusion of biological membranes results in two bilayer-based membranes merging into a single membrane. In this process the lipids have to undergo considerable rearrangement. The nature of the intermediates that are formed during this rearrangement has been investigated. Certain fusion proteins facilitate this process. In many cases short segments of these fusion proteins have a particularly important role in accelerating the fusion process. Studies of the interaction of model peptides with membranes have allowed for increased understanding at the molecular level of the mechanism of the promotion of membrane fusion by fusion proteins. There is an increased appreciation of the roles of several independent segments of fusion proteins in promoting the fusion process. Many of the studies of the fusion of biological membranes have been done with the fusion of enveloped viruses with other membranes. One reason for this is that the number of proteins involved in viral fusion is relatively simple, often requiring only a single protein. For many enveloped viruses, the structure of their fusion proteins has certain common elements, suggesting that they all promote fusion by an analogous mechanism. Some aspects of this mechanism also appears to be common to intracellular fusion, although several proteins are involved in that process which is more complex and regulated than is fusion.
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Ulmschneider, Martin. "Spontaneous Assembly of Functional Membrane Proteins from Soluble Membrane Active Peptides." Biophysical Journal 114, no. 3 (February 2018): 8a. http://dx.doi.org/10.1016/j.bpj.2017.11.080.
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Szabó, Zalán, Adriana Oliveira Stahl, Sonja-V. Albers, Jessica C. Kissinger, Arnold J. M. Driessen, and Mechthild Pohlschröder. "Identification of Diverse Archaeal Proteins with Class III Signal Peptides Cleaved by Distinct Archaeal Prepilin Peptidases." Journal of Bacteriology 189, no. 3 (November 17, 2006): 772–78. http://dx.doi.org/10.1128/jb.01547-06.
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ABSTRACT Most secreted archaeal proteins are targeted to the membrane via a tripartite signal composed of a charged N terminus and a hydrophobic domain, followed by a signal peptidase-processing site. Signal peptides of archaeal flagellins, similar to class III signal peptides of bacterial type IV pilins, are distinct in that their processing sites precede the hydrophobic domain, which is crucial for assembly of these extracytoplasmic structures. To identify the complement of archaeal proteins with class III signal sequences, a PERL program (FlaFind) was written. A diverse set of proteins was identified, and many of these FlaFind positives were encoded by genes that were cotranscribed with homologs of pilus assembly genes. Moreover, structural conservation of primary sequences between many FlaFind positives and subunits of bacterial pilus-like structures, which have been shown to be critical for pilin assembly, have been observed. A subset of pilin-like FlaFind positives contained a conserved domain of unknown function (DUF361) within the signal peptide. Many of the genes encoding these proteins were in operons that contained a gene encoding a novel euryarchaeal prepilin-peptidase, EppA, homolog. Heterologous analysis revealed that Methanococcus maripaludis DUF361-containing proteins were specifically processed by the EppA homolog of this archaeon. Conversely, M. maripaludis preflagellins were cleaved only by the archaeal preflagellin peptidase FlaK. Together, the results reveal a diverse set of archaeal proteins with class III signal peptides that might be subunits of as-yet-undescribed cell surface structures, such as archaeal pili.
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Rainey, Jan K., Larry Fliegel, and Brian D. Sykes. "Strategies for dealing with conformational sampling in structural calculations of flexible or kinked transmembrane peptidesThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB — Membrane Proteins in Health and Disease." Biochemistry and Cell Biology 84, no. 6 (December 2006): 918–29. http://dx.doi.org/10.1139/o06-178.
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Peptides corresponding to transmembrane (TM) segments from membrane proteins provide a potential route for the determination of membrane protein structure. We have determined that 2 functionally critical TM segments from the mammalian Na+/H+ exchanger display well converged structure in regions separated by break points. The flexibility of these break points results in conformational sampling in solution. A brief review of available NMR structures of helical membrane proteins demonstrates that there are a number of published structures showing similar properties. Such flexibility is likely indicative of kinks in the full-length protein. This minireview focuses on methods and protocols for NMR structure calculation and analysis of peptide structures under conditions of conformational sampling. The methods outlined allow the identification and analysis of structured peptides containing break points owing to conformational sampling and the differentiation between oligomerization and ensemble-averaged observation of multiple peptide conformations.
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Li, Caroline M., Pouya Haratipour, Robert G. Lingeman, J. Jefferson P. Perry, Long Gu, Robert J. Hickey, and Linda H. Malkas. "Novel Peptide Therapeutic Approaches for Cancer Treatment." Cells 10, no. 11 (October 27, 2021): 2908. http://dx.doi.org/10.3390/cells10112908.
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Peptides are increasingly being developed for use as therapeutics to treat many ailments, including cancer. Therapeutic peptides have the advantages of target specificity and low toxicity. The anticancer effects of a peptide can be the direct result of the peptide binding its intended target, or the peptide may be conjugated to a chemotherapy drug or radionuclide and used to target the agent to cancer cells. Peptides can be targeted to proteins on the cell surface, where the peptide–protein interaction can initiate internalization of the complex, or the peptide can be designed to directly cross the cell membrane. Peptides can induce cell death by numerous mechanisms including membrane disruption and subsequent necrosis, apoptosis, tumor angiogenesis inhibition, immune regulation, disruption of cell signaling pathways, cell cycle regulation, DNA repair pathways, or cell death pathways. Although using peptides as therapeutics has many advantages, peptides have the disadvantage of being easily degraded by proteases once administered and, depending on the mode of administration, often have difficulty being adsorbed into the blood stream. In this review, we discuss strategies recently developed to overcome these obstacles of peptide delivery and bioavailability. In addition, we present many examples of peptides developed to fight cancer.