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Infectious diseases kill over 17 million people a year, among which bacterial infections stand out. From all the bacterial infections, tuberculosis, diarrhoea, meningitis, pneumonia, sexual transmission diseases and nosocomial infections are the most severe bacterial infections, which affect millions of people worldwide. Moreover, the indiscriminate use of antibiotic drugs in the last decades has triggered an increasing multiple resistance towards these drugs, which represent a serious global socioeconomic and public health risk. It is estimated that 33,000 and 35,000 people die yearly in Europe and the United States, respectively, as a direct result of antimicrobial resistance. For all these reasons, there is an emerging need to find novel alternatives to overcome these issues and reduced the morbidity and mortality associated to bacterial infectious diseases. In that sense, nanotechnological approaches, especially smart polymeric nanoparticles, has wrought a revolution in this field, providing an innovative therapeutic alternative able to improve the limitations encountered in available treatments and capable to be effective by theirselves. In this review, we examine the current status of most dangerous human infections, together with an in-depth discussion of the role of nanomedicine to overcome the current disadvantages, and specifically the most recent and innovative studies involving polymeric nanoparticles against most common bacterial infections of the human body., Authors acknowledge the support of the Spanish Ministry of Economy and Competitiveness (SAF2017-84283-R and RTI2018-098641-B-I00), Biomedical Research Networking Centre in Neurodegenerative Diseases (CIBERNED, CB06/05/0024), Scientifc Project Marató TV3 (ref 201829-10) and European Regional Development Founds. Authors also acknowledge the Portuguese Science and Technology Foundation (FCT) for the strategic fund (UIDB/04469/2020)., info:eu-repo/semantics/publishedVersion

The amphipathic a-helical peptide KIA14 [(KIAGKIA)(2)-NH2] was studied in membranes using circular dichroism and solid-state NMR spectroscopy to obtain global as well as local structural information. By analyzing H-2 NMR data from 10 analogues of KIA14 that were selectively labeled with Ala-d(3), those positions that are properly folded into a helix could be determined within the membrane-bound peptide. The N-terminus was found to be unraveled, whereas positions 4-14 formed an ideal helix all the way to the C-terminus. The helicity did not change when Gly residues were replaced by Ala-d3 but was reduced when Ile was replaced, indicating that large hydrophobic residues are required for membrane binding and helix formation. The reduced helicity was strongly correlated with a decrease in peptide-induced leakage from lipid vesicles. The orientation of the short KIA14 peptide was assessed in several lipid systems and compared with that of the longer KIA21 sequence [(KIAGKIA)(3)-NH2]. In 1,2-dioleoylsn-glycero-3-phosphatidylcholine, both peptides are aligned flat on the membrane surface, whereas in 1,2-dimyristoyl-sn-glycero3-phosphatidylcholine (DMPC)/1-myristoy1-2-hydroxy-sn-glycero-3-phosphatidylcholine (lyso-MPC) both are inserted into the membrane in an upright orientation. These two types of lipid systems had been selected for their strongly negative and positive spontaneous curvature, respectively. We propose that in these cases, the peptide orientation is largely determined by the lipid properties. On the other hand, in plain DMPC and 1,2-dilauroyl-sn-glycero-3-phosphatidylcholine, which have only a slight positive curvature, a marked difference in orientation is evident: the short KIA14 lies almost flat on the membrane surface, whereas the longer KIA21 is more tilted. We thus propose that out of the lipid systems tested here, DMPC (with hardly any curvature) is the least biased,lipid system in which peptide orientation and realignment can be studied, allowing to compare and discriminate the intrinsic effects of the properties of the peptides as such.

Bacillus methylotrophicus DCS1 strain was isolated from diesel contaminated soil and screened for its ability to produce biosurfactants; it was found effective for the production of surface active molecules. The structural characterization of the isolated lipopeptides was studied by a variety of analytical techniques. The organic extract of DCS1 'lipopeptides was fractionated by silica gel column chromatography (60 Mesh). Fractions containing lipopeptides were collected and identified by tandem mass spectrometry MALDI-TOF-MS and MALDI-TOF MS2. The crude biosurfactants contains a mixture of homologous lipopeptides with molecular weights between 1016 and 1556 Da. Mass spectrometry analysis of partially purified lipopeptides revealed that it contains different isoforms belonging to three families: surfactin, iturin and fengycin. To identify lipopeptides isoforms, MALDI-TOF MS2 was used and ions representing characteristic fragmentations were detected. The mass spectrometry characterization revealed the presence of four variants of surfactin lipopeptides, four variants of pumilacidin that differ according to the-beta-hydroxy fatty acid chain length as well as the type of amino acid at position 7, five variants of iturin A/mycosubtilin varying in the beta-amino fatty acid chain length from C12 to C16, C16 iturin Cl, five isoforms of bacillomycin D varying in the beta-amino fatty acid chain length from C14 to C18, and six fengycin isoforms that differ according to the length of the beta-hydroxy fatty acid side chain as well as the amino acid at position 6. The capacity of B. methylotrohicus DCS1 strain to produce many lipopeptides isoforms belonging to different families and having a structural diversity is a very interesting characteristic that allows them to be used in various fields of biotechnological applications.

Hydrophobic mismatch is important for pore forming amphipathic antimicrobial peptides, as demonstrated recently [Grau-Campistany, A., et al. (2015) Sci. Rep. 5, 9388]. A series of different length peptides have been generated with the heptameric repeat sequence KIAGKIA, called KIA peptides, and it was found that only those helices sufficiently long to span the hydrophobic thickness of the membrane could induce leakage in lipid vesicles; there was also a clear length dependence of the antimicrobial and hemolytic activities. For the original KIA sequences, the cationic charge increased with peptide length. The goal of this work is to examine whether the charge also has an effect on activity; hence, we constructed two further series of peptides with a sequence similar to those of the KIA peptides, but with a constant charge of +7 for all lengths from 14 to 28 amino acids. For both of these new series, a clear length dependence similar to that of KIA peptides was observed, indicating that charge has only a minor influence. Both series also showed a distinct threshold length for peptides to be active, which correlates directly with the thickness of the membrane. Among the longer peptides, the new series showed activities only slightly lower than those of the original KIA peptides of the same length that had a higher charge. Shorter peptides, in which Gly was replaced with Lys, showed activities similar to those of KIA peptides of the same length, but peptides in which Ile was replaced with Lys lost their helicity and were less active.

In this work, the extraction, structural analysis, and identification as well as antimicrobial, anti-adhesive, and antibiofilm activities of lipopeptides produced by Enterobacter cloacae C3 strain were studied. A combination of chromatographic and spectroscopic techniques offers opportunities for a better characterization of the biosurfactant structure. Thin layer chromatography (TLC) and HPLC for amino acid composition determination are used. Efficient spectroscopic techniques have been utilized for investigations on the biochemical structure of biosurfactants, such as Fourier transform infrared (FT-IR) spectroscopy and mass spectrometry analysis. This is the first work describing the production of different isoforms belonging to kurstakin and surfactin families by E cloacae strain. Three kurstakin homologues differing by the fatty acid chain length from C10 to C12 were detected. The spectrum of lipopeptides belonging to surfactin family contains various isoforms differing by the fatty acid chain length as well as the amino acids at positions four and seven. Lipopeptide C3 extract exhibited important antibacterial activity against Gram-positive and Gram-negative bacteria, antifungal activity, and interesting anti-adhesive and disruptive properties against biofilm formation by human pathogenic bacterial strains: Salmonella typhimurium, Klebsiella pneumoniae, Staphylococcus aureus, Bacillus cereus, and Candida albicans.

A halotolerant strain CO100 of Staphylococcus sp. was isolated from contaminated sediments taken from the fishing harbour of Sfax, Tunisia, as an efficient hydrocarbonoclastic candidate. Strain CO100 exhibited a high capacity to break down almost 72% of the aliphatic hydrocarbons contained in crude oil (1%, v/v), used as the sole carbon and energy source, after 20 days of culture, at 100 g/l NaCl, 37 °C and 180 rpm. The isolate CO100 displayed also its ability to grow on phenanthrene, fluoranthene and pyrene (100 mg/l), at 100 g/l NaCl. Moreover, the isolate CO100 showed a notable aptitude to synthesize an efficient tensioactive agent namely BS-CO100, on low-value substrates including residual frying oil and expired milk powder, thus reducing the high cost of biosurfactant production. The ESI/MS analysis designated that BS-CO100 belonged to lipopeptide class, in particular lichenysin and iturine members. Critical micelle concentrations of BS-CO100 were varying between 65 and 750 mg/l, depending on of the purity of the biosurfactant and the used carbon sources. BS-CO100 showed a high steadiness against a wide spectrum of pH (4.3–12), temperature (4–121 °C) and salinity (0–300 g/l NaCl), supporting its powerful tensioactive properties under various environmental conditions. Likewise, BS-CO100 exhibited no cytotoxic effect toward human HEK293 cells, at concentrations within 125 and 1000 μg/ml. Furthermore, the biosurfactant BS-CO100 exhibited remarkable anti-adhesive and anti-biofilm activities, being able to avoid and disrupt the biofilm formation by certain pathogenic microorganisms. In addition, BS-CO100 was found to have more potential to remove hydrocarbons from contaminated soils, compared to some chemical surfactants. In light of these promising findings, strain CO100, as well as its biosurfactant, could be successfully used in different biotechnological applications including the bioremediation of oil-polluted areas, even under saline conditions.

Resistance to all known antibiotics is a growing concern worldwide, and has renewed the interest in antimicrobial peptides, a structurally diverse class of amphipathic molecules that essentially act on the bacterial membrane. Propelled by the antimicrobial potential of this compound class, we have designed three new lipopeptides derived from polymyxin B, sp-34, sp-96 and sp-100, with potent antimicrobial activity against both Gram positive and Gram negative bacteria. The three peptides bind with high affinity to lipopolysaccharide as demonstrated by monolayer penetration and dansyl-displacement. The interaction with the cytoplasmic membrane has been elucidated by biophysical experiments with model membranes of POPG or POPE/POPG (6:4), mimicking the Gram positive and Gram negative bacterial membrane. Trp-based fluorescence experiments including steady-state, quenching, anisotropy and FRET, reveal selectivity for anionic phospholipids and deep insertion into the membrane. All three lipopeptides induce membrane fusion and leakage from anionic vesicles, a process that is favored by the presence of POPE. The molecules bind to zwitterionic POPC vesicles, a model of the eukaryotic membrane, but in a different way, with lower affinity, less penetration into the bilayer and no fusion or permeabilization of the membrane. Results in model membranes are consistent with flow cytometry experiments in Escherichia coli and Staphylococcus aureus using a membrane potential sensitive dye (bis-oxonol) and a nucleic acid dye (propidium iodide), suggesting that the mechanism of action is based on membrane binding and collapse of membrane integrity by depolarization and permeabilization. (C) 2015 Elsevier B.V. All rights reserved.

Background Staphylococcus aureus, including 'superbug' MRSA, is a major cause of nosocomial infections. In the European Union, up to 171 200 new nosocomial MRSA infections are acquired annually, and in the USA S. aureus causes more deaths than HIV/AIDS and tuberculosis combined. MRSA is also the first group of pathogens that infect the pulmonary tract in young patients with cystic fibrosis. Objectives We describe two newly developed and synthesized colistin (polymyxin E)-inspired molecules. Methods A collection of several isolates of S. aureus [including MRSA and vancomycin-resistant S. aureus (VRSA)] was tested. To check the antimicrobial activity, we performed time-kill curves, growth curves, biofilm eradication, toxicity and isothermal titration calorimetry. Results Both peptides showed high antimicrobial activities (MIC 4 mg/L) and low relative toxicities (selectivity index close to 23). Conclusions Successful production of polymyxin-scaffold molecules active against S. aureus, both MRSA and VRSA, opens up new approaches to the treatment of these complicated infections.

Biosurfactants are of great interest due to the demand for natural products with low toxicity. Nevertheless, their production is not competitive when cost is a limiting factor. Strain AL 1.1, isolated on Deception Island (Antarctica), identified as Bacillus licheniformis, produced lipopeptides when grown using a variety of carbohydrates. Biosurfactant production, but not growth, was optimal at 30 °C. The culture conditions and medium composition dictated biosurfactant production. Basic optimization of culture and extraction parameters gave a production yiels of 860 mg/L purified extract in 24 h. The purified biosurfactant yielded a mixture of lipopeptide homologues, with molecular weights between 1006 and 1034. The peptide moiety consists of glutamine as the N-terminal amino acid, two leucines, valine, aspartic, leucine and isoleucine as the C-terminal amino acid. The lipid moiety contains a mixture of β-hydroxy fatty acids ranging in size from C14 to C16. These results indicate a similarity with lichenysin groups A, D or G. The organic extract reduced surface tension to 28.5 mN/m and achieved a critical micelle concentration of 15 mg/L. This highly effective and efficient behavior characterized the product as a powerful surfactant. Its stability under a wide pH range, high temperatures and variable concentrations of salt, as well as its emulsifying properties, suggest potential application in cosmetic industrial processes.

There is a clear unmet medical need in the field of infectious diseases: infections caused by resistant bacteria. A major goal to fight resistant bacteria involves the design, discovery and development of new antibiotics particularly against multi-drug-resistant strains. Polymyxins, an old class of antimicrobial cyclic lipopeptides highly potent against therapeutically relevant Gram-negative bacteria, have been rescued and are now used only as last resort antibiotics in hospitals because of their nephrotoxicity and neurotoxicity that require careful monitoring of the patient. Our group has embarked in a project to design and develop new polymyxins devoid of toxicity problems using a versatile and chemically accessible scaffold structure[1,2]. Compounds show a remarkable activity against Gram-negative bacteria. Synergistic and antibiofilm activities have also been recently described in combination with imipenem[3]. Herein, the last results of our recently designed polymyxin analogs will be presented. References F. Rabanal, A. Grau-Campistany, X. Vila-Farres, J. Gonzalez-Linares, M. Borras, J. Vila, A. Manresa and Y. Cajal. A bioinspired peptide scaffold with high antibiotic activity and low in vivo toxicity, Sci. Rep., 2015, 5, 10558. https://www.nature.com/articles/srep10558 F. Rabanal, Y. Cajal, Recent advances and perspectives in the design and development of polymyxins. Natural Product Reports, 34, 886 - 908 (2017) http://pubs.rsc.org/en/content/articlelanding/2017/np/c7np00023e#!divAbstract H. Rudilla, E. Fuste, Y. Cajal, F. Rabanal, T. Vinuesa and M. Vinas, Synergistic Antipseudomonal Effects of Synthetic Peptide AMP38 and Carbapenems, Molecules, 2016, 21, 1223. http://www.mdpi.com/1420-3049/21/9/1223

Antimicrobial peptides offer a new class of therapeutic agents to which bacteria may not be able to develop genetic resistance, since they act on the lipid component of the cell membranes [1]. [...]

Antibiotic resistance is a daunting challenge for public health systems worldwide. [...]

INTRODUCTION: The recent dramatic increase in the incidence of antimicrobial resistance has been recognized by organizations such as the United Nations and World Health Organization as well as the governments of the USA and several European countries. A relatively new weapon in the fight against severe infections caused by multi-drug resistant bacteria is antimicrobial peptides (AMPs). These include colistin, currently regarded as the last line of antimicrobial therapy against multi-drug resistant microorganisms. Areas covered: Here, the authors provide an overview of the current research on AMPs. The focus is AMPs currently being developed for the treatment of recalcitrant bacterial infections, the synergies of AMPs and antibiotics, and the activity of AMPs against biofilm. This review also includes a brief introduction into the use of AMPs in infections caused by Mycobacterium, fungi, and parasites. Expert opinion: In research into new antimicrobials, AMPs are gaining increasing attention. While many are natural and are produced by a wide variety of organisms, others are being newly designed and chemically synthesized in the laboratory to achieve novel antimicrobial agents. The same strategy to fight infections in nature is thus being effectively exploited to safeguard human and animal health.

Covering: 1947-early 2017, particularly from 2005-early 2017 The rise of bacterial pathogens with acquired resistance to almost all available antibiotics is becoming a serious public health issue. Polymyxins, antibiotics that were mostly abandoned a few decades ago because of toxicity concerns, are ultimately considered as a last-line therapy to treat infections caused by multi-drug resistant Gram-negative bacteria. This review surveys the progress in understanding polymyxin structure, and their chemistry, mechanisms of antibacterial activity and nephrotoxicity, biomarkers, synergy and combination with other antimicrobial agents and antibiofilm properties. An update of recent efforts in the design and development of a new generation of polymyxin drugs is also discussed. A novel approach considering the modification of the scaffold of polymyxins to integrate metabolism and detoxification issues into the drug design process is a promising new line to potentially prevent accumulation in the kidneys and reduce nephrotoxicity.

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A series of nine amphiphilic, pore-forming α-helical KIA peptides (KIAGKIA repeats) with lengths between 14 and 28 residues were studied by solid-state (15)N NMR to determine their alignment in oriented lipid bilayers. In a 2:1 mixture of 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine (DMPC) with its corresponding 1-myristoyl-2-hydroxy-sn-glycero-3-phosphocholine (lyso-MPC), which has a highly positive spontaneous curvature, the helix tilt angle was found to vary steadily with peptide length. The shortest peptide was aligned transmembrane and upright, while the longer ones successively became tilted away from the membrane normal. This behavior is in agreement with the hydrophobic matching concept, conceived so far only for hydrophobic helices. In 1,2-dioleoyl-sn-glycero-3-phosphatidylcholine, with a negative spontaneous curvature, all KIA peptides remained flat on the bilayer surface, while the cylindrical DMPC lipids permitted a slight tilt. Peptide insertion thus depends critically on the intrinsic lipid curvature, and helix orientation is then fine-tuned by membrane thickness. A refined toroidal pore model is proposed.

The emergence of pathogens which are resistant or multi-drug resistant to most of the currently available antibiotics is posing an immense burden to the healthcare systems throughout the world. The development of new classes of antibiotics has also suffered a decline since many pharmaceutical companies have gradually abandoned the field. Fortunately, several public–private initiatives to spur the development of new antibiotics have been recently launched. Antimicrobial peptides are thus attracting a renewed interest as potential therapeutic antibiotic candidates. In fact, some of the oldest available antibiotics in the market are cyclic antimicrobial peptides, such as polymyxin B, colistin, gramicidin or bacitracin. However, pharmacological and toxicological problems associated with the systemic use of antimicrobial peptides are slowing their development and drug approval. An overview of the advantages and drawbacks of antimicrobial peptides as antibiotic drugs and a report of compounds that are in development are described.

An emerging and attractive target for the treatment of Alzheimer's disease is to inhibit the aggregation of beta-amyloid protein (Abeta). We applied the retro-enantio concept to design an N-methylated peptidic inhibitor of the Abeta42 aggregation process. This inhibitor, inrD, as well as the corresponding all-L (inL) and all-D (inD) analogues were assayed for inhibition of Abeta42 aggregation. They were also screened in neuroblastoma cell cultures to assess their capacity to inhibit Abeta42 cytotoxicity and evaluated for proteolytic stability. The results reveal that inrD and inD inhibit Abeta42 aggregation more effectively than inL, that inrD decreases Abeta42 cytotoxicity to a greater extent than inL and inD, and that as expected, both inD and inrD are stable to proteases. Based on these results, we propose that the retro-enantio approach should be considered in future designs of peptide inhibitors of protein aggregation.

The aim of this study was to design synthetic peptides with D-amino acid substitutions that mimic the human immunodeficiency virus (HIV) gp41 HR2 region. The objective was to develop new and active C34 analogue peptides by introducing D-amino acid point substitutions at nonessential sites for HR1-HR2 interaction without disrupting the structure of the peptide. Herein we report a study with C34L peptide analogues, including the enantiomer peptide C34D, the retro-inverso analogue (RI), and two peptides with D-amino acid point substitutions (C34M2 and C34M3). Our results show that, with the exception of RI, these peptides adopt an alpha-helical structure and are, like C34L, able to interact with HR1, mimicked by the N36 peptide. Furthermore, we show that modifications introduced in C34M2, but not in C34M3, enhance its resistance to trypsin-mediated hydrolysis and increase the stability of C34M2 in physiological medium. Interestingly, our results show that C34 peptide analogues C34M2 and C34M3, but not C34D and its RI analogue, retain their ability to inhibit HIV-1 replication with an efficiency similar to that of the C34L peptide. These data underscore the interest in using D-amino acids at specific sites in the C34 peptide sequence and may lead to a new strategy for the development of more stable and active anti-HIV-1 peptidic drugs.

A novel combinatorial strategy for the redesign of proteins based on the strength and specificity of intra- and interprotein interactions is described. The strategy has been used to redesign the hydrophobic core of the B domain of protein A. Using one-bead-one-compound combinatorial chemistry, 300 analogues of the C-terminal alpha-helix of the B domain, H3x, have been synthesized using a biocompatible resin and the HMFS linker, allowing the screening to occur while the peptides were bound to the resin. The screening was based on the ability of the H3x analogues to interact with the N-terminal helices of the B domain, H1-H2, and retain the native B domain activity, that is binding to IgG. Eight different analogues containing some nonconservative mutations were obtained from the library, the two most frequent of which, H3P1 and H3P2, were studied in detail. CD analysis revealed that the active analogues interact with H1-H2. To validate the redesign strategy the covalent modified domains H1-H2-H3P1 and H1-H2-H3P2 were synthesized and characterized. CD and NMR analysis revealed that they had a unique, stable, and well-defined three-dimensional structure similar to that for the wild-type B domain. This combinatorial strategy allows us to select for redesigned proteins with the desired activity or the desired physicochemical properties provided the right screening test is used. Furthermore, it is rich in potential for the chemical modification of proteins overcoming the drawbacks associated with the total synthesis of large protein domains.

[Structure: see text] A procedure for the preparation of proline N-carboxyanhydride in high yield and purity is described using polymer-supported tertiary amines. The polymer-supported amine can be recycled with a basic wash and filtration of the resin. The procedure facilitates the access to the efficient preparation of the polyproline polymer with potential therapeutic interest.

We have designed synthetic peptides that mimic the primary and secondary structure of the cationic lipopeptide antibiotic polymyxin B (PxB) in order to determine the structural requirements for membrane action and to assess possible therapeutic potential. Two analogues with related sequences to that of PxB, but including synthetic simplifications (disulphide bridge between two cysteines in positions 4 and 10, N-terminal nonanoic acid), have been synthesized. Peptide-lipid interactions have been studied by fluorescence resonance energy transfer between pyrene and 4,4-difluoro-5-methyl-4-bora-3alpha,4alpha-diaza-s-indacene-3-dodecanoyl (BODIPY)probes covalently linked to phospholipids, and the possibility of membrane disruption or permeabilization has been assessed by light scattering and fluorescence quenching assays. The synthetic peptide sP-B, which closely mimics the primary and secondary structures of PxB, binds to vesicles of anionic 1-palmitoyl-2-oleoylglycero-sn-3-phosphoglycerol (POPG) or of lipids extracted from Escherichia coli membranes, and induces apposition of the vesicles and selective lipid exchange without permeabilization of the membrane. We conclude that sP-B forms functional vesicle-vesicle contacts that are selective, as previously described for PxB. The second analogue, sP-C, has a permutation of two amino acids that breaks the hydrophobic patch formed by D-Phe and Leu residues on the cyclic part of the sequence. sP-C lipopeptide is more effective than sP-B in inducing lipid mixing, but shows no selectivity for the lipids that exchange through the vesicle-vesicle contacts, and at high concentrations has a membrane-permeabilizing effect. The deacylated and non-antibiotic derivative PxB-nonapeptide (PxB-NP) does not induce the formation of functional intervesicle contacts in the range of concentrations studied.

We have used solid state NMR to study the orientation of membrane-active peptides in model membranes with different properties. We found that the peptide behavior can to a large extent be explained by the simple biophysical concepts of hydrophobic matching and lipid spontaneous curvature. Hydrophobic peptides insert in the membrane in a transmembrane orientation, and it is well established that peptides which have a longer hydrophobic stretch than the bilayer thickness start to tilt to compensate the hydrophobic mismatch. Here we show that the hydrophobic matching principle also applies to cationic amphipathic α-helical antimicrobial peptides. Using a series of peptides called KIAn, based on the repetitive amino acid sequence KIAGKIA, we found that only peptides long enough to span the hydrophobic thickness of the membrane induce leakage in lipid vesicles. Interestingly, a certain minimum length was also needed to induce hemolysis and to kill bacteria, and this minimum length was different for different bacterial strains, so that the series of peptides can be used as a “molecular ruler” to determine the thickness of erythrocyte or bacterial membranes in vivo. Using solid-state NMR we found that the orientation depends strongly on the lipid spontaneous curvature. The KIA peptides are always staying flat on the membrane surface in lipids with a negative spontaneous curvature. On the other hand, in lipids with a positive spontaneous curvature, like lyso-lipids, they can go deeper into the membrane and have a tilted or even inserted orientation. In the inserted state, the tilt of the peptides is found to be mismatch dependent. This is the first time a mismatch effect has been found for amphipathic peptides, and shows that the effect is more generally valid than has been appreciated until now.

Antimicrobial peptides offer a new class of therapeutic agents to which bacteria may not be able to develop genetic resistance, since their main activity is in the lipid component of the bacterial cell membrane. We have developed a series of synthetic cationic cyclic lipopeptides based on natural polymyxin, and in this work we explore the interaction of sp-85, an analog that contains a C12 fatty acid at the N-terminus and two residues of arginine. This analog has been selected from its broad spectrum antibacterial activity in the micromolar range, and it has a disruptive action on the cytoplasmic membrane of bacteria, as demonstrated by TEM. In order to obtain information on the interaction of this analog with membrane lipids, we have obtained thermodynamic parameters from mixed monolayers prepared with POPG and POPE/POPG (molar ratio 6:4), as models of Gram positive and Gram negative bacteria, respectively. Langmuir–Blodgett films have been extracted on glass plates and observed by confocal microscopy, and images are consistent with a strong destabilizing effect on the membrane organization induced by sp-85. The effect of sp-85 on the membrane is confirmed with unilamelar lipid vesicles of the same composition, where biophysical experiments based on fluorescence are indicative of membrane fusion and permeabilization starting at very low concentrations of peptide and only if anionic lipids are present. Overall, results described here provide strong evidence that the mode of action of sp-85 is the alteration of the bacterial membrane permeability barrier.

The optimization of a synthetic process for the preparation of HMFS handle, which is used for the solid-phase synthesis of peptides and oligonucleotides, is presented.

Aspartimide prone sequence containing protected peptides are successfully synthesized in solid phase by using the bifunctional linker N-[(9-hydroxymethyl)-2-fluorenyl] succinamic acid (HMFS) in combination with morpholine as the cleavage reagent. Access to high purity peptide synthons opens a straightforward way to the synthesis of large proteins by convergent strategies.

Heme A, a prosthetic group of cytochrome c oxidase [EC 1.9.3.1], has been introduced into two de novo designed four helix bundle proteins, [H10A24](2) and [H10H24](2), known to bind 2-4 equiv of heme B, respectively [Robertson, D. E., Farid, R. S., Moser, C. C., Mulholland, S. E., Pidikiti, R., Lear, J. D., Wand, A., J., DeGrado, W. F., and Dutton, P. L. (1994) Nature 368, 425-432]. [H10A24](2), [Ac-CGGGELWKL x HEELLKK x FEELLKL x AEERLKK x L-CONH(2)](2)(2), binds two heme A molecules per four-helix unit via bis-histidine ligation at the 10,10' positions with measured K(d) values of

The prototype ferredoxin maquette, FdM, is a 16-amino acid peptide which efficiently incorporates a single [4Fe-4S]2+/+ cluster with spectroscopic and electrochemical properties that are typical of natural bacterial ferredoxins. Using this synthetic protein scaffold, we have investigated the role of the nonliganding amino acids in the assembly of the iron-sulfur cluster. In a stepwise fashion, we truncated FdM to a seven-amino acid peptide, FdM-7, which incorporates a cluster spectroscopically identical to FdM but in lower yield, 29% relative to FdM. FdM-7 consists solely of the. CIACGAC. consensus ferredoxin core motif observed in natural protein sequences. Initially, all of the nonliganding amino acids were substituted for either glycine, FdM-7-PolyGly (.CGGCGGC.), or alanine, FdM-7-PolyAla (.CAACAAC.), on the basis of analysis of natural ferredoxin sequences. Both FdM-7-PolyGly and FdM-7-PolyAla incorporated little [4Fe-4S]2+/+ cluster, 6 and 7%, respectively. A systematic study of the incorporation of a single isoleucine into each of the four nonliganding positions indicated that placement either in the second or in the sixth core motif positions,.CIGCGGC. or.CGGCGIC., restored the iron-sulfur cluster binding capacity of the peptides to the level of FdM-7. Incorporation of an isoleucine into the fifth position,.CGGCIGC., which in natural ferredoxins is predominantly occupied by a glycine, resulted in a loss of [4Fe-4S] affinity. The substitution of leucine, tryptophan, and arginine into the second core motif position illustrated the stabilization of the [4Fe-4S] cluster by bulky hydrophobic amino acids. Furthermore, the incorporation of a single isoleucine into the second core motif position in a 16-amino acid ferredoxin maquette resulted in a 5-fold increase in the level of [4Fe-4S] cluster binding relative to that of the glycine variant. The protein design rules derived from this study are fully consistent with those derived from natural ferredoxin sequence analysis, suggesting they are applicable to both the de novo design and structure-based redesign of natural proteins.

An iterative redesign protocol for the transformation of a non-native peptide into a series of nativelike proteins derived from elementary considerations of biological evolution coupled with 1H NMR as an artificial selection criterion is presented. Each of three heptad d position leucines in the helix−helix interfaces of the prototype heme protein maquette, [H10H24]2 or (α-SS-α)2, were replaced in a unit modification per helix by more conformationally restricted β-branched and aromatic amino acids. The secondary structure content (evaluated by circular dichroism and infrared spectroscopies), solvent accessibility of the tryptophan residues (measured by fluorescence spectroscopy), global stability (quantitated by isothermal chemical denaturation), and degree of conformational specificity (determined by 1H NMR spectroscopy) of the resultant peptides were determined. Improvement in the degree of conformational specificity was utilized as a selection criterion to choose three of the nine singly modified pepti...

The solution structure of a de novo designed disulfide-bridged two-R-helix peptide that self-assembles to form a 2-fold symmetric four-R-helix bundle protein (R'-SS-R')2 has been solved by NMR spectroscopy. The 33-residue peptide, (R'-SH), that is the basic building block of the bundle has been recombinantly expressed. The three-dimensional structure of the asymmetric unit of the bundle has been determined using interproton distance restraints derived from the nuclear Overhauser effect (NOE), covalent torsion angle restraints derived from three bond scalar coupling constants, and longer range angular restraints derived from residual dipolar couplings. The covalent R'-SS-Runit forms a pair of parallel R-helices that use heptad a-, d-, e-, and g-side chains to form a hydrophobic core extending the length of the molecule. The distribution of polar and nonpolar side chains on the surface of R'-SS-Rstructure is asymmetric. The hydrophilic face is comprised of glutamate and lysine side chains, while the opposite face is comprised of leucine, isoleucine, phenylalanine, tryptophan, and neutral histidine side chains. Equilibrium sedimentation analysis, size-exclusion chromatography, pulsed field gradient translation diffusion measurements, and a rotational correlation time derived from 15 N NMR relaxation studies all indicate that the covalent R'-SS-Runit forms a noncovalent dimer, (R'-SS-R')2, in solution. The structure confirms many expected design features and illuminates an apparent dichotomy of structure where the helical interface of the disulfide bridged two- R-helix peptide appears nativelike while the adjacent, noncovalent interface shows non-nativelike behavior. Available evidence indicates the four R-helix bundle can adopt either an anti or syn topology. The structure is discussed with respect to the potential origins of conformational specificity and nativelike protein structure.

A survey of ferredoxin maquettes derived from natural sequences was utilized to obtain a primary sequence competent for [4Fe-4S]2+/+ incorporation for the study of the minimal ligand requirements f...

N,N′-disuccinimidyl carbonate (DSC) has been successfully used to generate carbonates and carbamates on conventional hydroxymethyl and aminomethyl based resins. This methodology extends the applicability of such linkers, which were initially designed for the anchoring of carboxylic acids. Thus, amino and hydroxy groups have been attached onto classical resins to give straightforward access to the solid-phase synthesis of alcohols, carbamates, and cyclic peptides with an evident pharmaceutical interest.

We have designed two alternative four helix bundle protein scaffold topologies for maquette construction to examine the effect of helix orientation on the heme binding and redox properties of our prototype heme protein maquette, (alpha-SS-alpha)2, previously described as H10H24 [Robertson, D. E., Farid, R. S., Moser, C. C., Mulholland, S. E., Pidikiti, R., Lear, J. D., Wand, A. J., DeGrado, W. F., and Dutton, P. L. (1994) Nature 368, 425]. Conversion of the disulfide-bridged di-alpha-helical monomer of (alpha-SS-alpha)2 into a single polypeptide chain results in topological reorientation of the helix dipoles and side chains within a 62 amino acid helix-loop-helix monomer, (alpha-l-alpha), which self-associates to form (alpha-l-alpha)2. Addition of an N-terminal cysteine residue to (alpha-l-alpha) with subsequent oxidation yields a 126 amino acid single molecule four helix bundle, (alpha-l-alpha-SS-alpha-l-alpha). Gel permeation chromatography demonstrated that (alpha-SS-alpha)2 and (alpha'-SS-alpha')2, a uniquely structured variant of the prototype, as well as (alpha-l-alpha)2 and (alpha'-l-alpha')2 assemble into distinct four helix bundles as designed, whereas (alpha-l-alpha-SS-alpha-l-alpha) elutes as a monomeric four alpha-helix bundle. Circular dichroism (CD) spectroscopy proves that these peptides are highly alpha-helical, and incorporation of four hemes has little effect on the helical content of the secondary structure. Four heme dissociation constants were evaluated by UV-visible spectroscopy and ranged from the 15 nM to 25 microM range for each of the peptides. The presence of Cotton effects in the visible CD illustrated that the hemes reside within the protein architecture. The equilibrium redox midpoint potentials (Em8) of the four bound hemes in each peptide are between -100 and -280 mV, as determined by redox potentiometry. The heme affinity and spectroelectrochemical properties of the hemes bound to (alpha-l-alpha)2 and (alpha-l-alpha-SS-alpha-l-alpha) are similar to those of the prototype, (alpha-SS-alpha)2, and to bis-histidine ligated b-type cytochromes, regardless of the global architectural changes imposed by these topological rearrangements. The hydrophobic cores of these peptides support local electrostatic fields which result in nativelike heme chromophore properties (spectroscopy, elevated reduction potentials, heme-heme charge interaction, and reactivity with exogenous diatomics) illustrating the utility of these non-native peptides in the study of metalloproteins.

To better understand the relation between structure and function of complex natural heme proteins, we have designed and synthesized de novo simplified versions called maquettes. Furthermore, we have assembled organized monolayers of these heme protein maquettes onto silanized quartz to more define their structural and functional properties and to take the first step in constructing robust devices that exploit biological chemistry. First, two di-α-helical peptides, α2, were designed and synthesized to self-assemble into a four-helix bundle [α2]2. The assembly has a well-developed hydrophobic interior and coordinates iron protoporphyrin IX (heme) by bis-histidine ligation. The chemisorption of these synthetic hemoproteins onto silanized quartz was achieved by reacting disulfide bridges in the loop region of each α2 with thiols immobilized at the surface. Self-assembled monolayers of synthetic hemoproteins were characterized by UV/vis spectroscopy. UV absorption of the tryptophan reveals the presence of pept...

The structural features of protein binding sites for volatile anesthetics are being explored using a defined model system consisting of a four-R-helix bundle scaffold with a hydrophobic core. Earlier work has demonstrated that a prototype hydrophobic core is capable of binding the volatile anesthetic halothane. Exploratory work on the design of an improved affinity anesthetic binding site is presented, based upon the introduction of a simple cavity into a prototype (R2)2 four-R-helix bundle by replacing six core leucines with smaller alanines. The presence of such a cavity increases the affinity ( Kd ) 0.71 ( 0.04 mM) of volatile anesthetic binding to the designed bundle core by a factor of 4.4 as compared to an analogous bundle core lacking such a cavity (Kd ) 3.1 ( 0.4 mM). This suggests that such packing defects present on natural proteins are likely to be occupied by volatile general anesthetics in ViVo. Replacing six hydrophobic core leucine residues with alanines results in a destabilization of the folded bundle by 1.7-2.7 kcal/mol alanine, although the alanine-substituted bundle still exhibits a high degree of thermodynamic stability with an overall folded conformational ¢G H2O ) 14.3 ( 0.8 kcal/mol. Covalent attachment of the spin label MTSSL to cysteine residues in the alanine-substituted four- R-helix bundle indicates that the di-R-helical peptides dimerize in an anti orientation. The rotational correlation time of the four-R-helix bundle is 8.1 ( 0.5 ns, in line with earlier work on similar peptides. Fluorescence, far-UV circular dichroism, and Fourier transform infrared spectroscopies verified the hydrophobic core location of the tryptophan and cysteine residues, showing good agreement between experiment and design. These small synthetic proteins may prove useful for the study of the structural features of small molecule binding sites. The site(s) of action of the volatile general anesthetics remain(s) unknown, despite over a century of active inves- tigation. Extensive studies on how anesthetics might alter the physical properties of the lipid component of membranes have shown only minor effects. Current consensus therefore favors membrane proteins as the targets for volatile anesthet- ics (1, 2). In line with this, a number of investigators have shown that volatile anesthetics alter the function of both voltage-gated (3) and ligand-gated ion channels (4) and also ion transport proteins (5). These studies demonstrate that anesthetics are capable of altering the actiVity of a number of different membrane proteins. However, it remains to be determined whether these functional changes follow directly from anesthetic binding to the proteins in question or are an indirect effect due to changes in the properties of membrane lipids.

De novo and rational protein design are progressing towards the chemical synthesis of proteins with pre-selected structure and function. The data illustrate diverse experimental and computational approaches which test our comprehension of protein structure, hydrophobic core packing and global stability, especially of coiled-coil proteins. The incorporation of biological cofactors, including hemes, as well as active sites, such as that of iron superoxide dismutase, into designed proteins provides an exciting next step towards the synthesis of proteins with enzymatic function.

N , N ′-Disuccinimidyl carbonate (DSC) has been successfully used for the efficient conversion of 4-hydroxymethylpolystyrene and 4-hydroxymethyl-3-nitrobenzamido (Nbb) resins into active carbonate resins, which are suitable for the incorporation of molecules via a hydroxyl function. This methodology has been applied to the preparation of the growth hormone inhibitor, Sandostatin.

A 16-amino acid residue peptide derived from a consensus motif of natural ferredoxins incorporates a tetranuclear iron sulfur cluster under physiological conditions. Successful assembly of the [4Fe–4S] 2+/1+ cluster within a monomeric peptide was demonstrated using size exclusion chromatography, UV-visible, visible CD, and cryogenic EPR spectroscopies. The robustness of [4Fe–4S] 2+/1+ formation was tested using peptides with either the ligating cysteine exchanged for alanine or with the intervening amino acids replaced by glycine. The small size of the peptide allows for modular incorporation into more complex protein structures. In one larger structure, we describe a tetra-α-helix bundle that self-assembles both iron–sulfur clusters and hemes, thereby demonstrating feasibility for the general synthesis of maquettes containing multiple, juxtaposed redox cofactors. This is a motif common to the catalytic sites of native oxidoreductases.