Sodium dodecyl sulfate monomers induce XAO peptide polyproline II to α-helix transition

Purification and Characterization of Novel Anti-MRSA Peptides Produced by Brevibacillus sp. SPR-20

Methicillin-resistant Staphylococcus aureus (MRSA) is listed as a high-priority pathogen because its infection is associated with a high mortality rate. It is urgent to search for new agents to treat such an infection. Our previous study isolated a soil bacterium (Brevibacillus sp. SPR-20), showing the highest antimicrobial activity against S. aureus TISTR 517 and MRSA strains. The present study aimed to purify and characterize anti-MRSA substances produced by SPR-20. The result showed that five active substances (P1-P5) were found, and they were identified by LC-MS/MS that provided the peptide sequences of 14-15 residues. Circular dichroism showed that all peptides contained β-strand and disordered conformations as the major secondary structures. Only P1-P4 adopted more α-helix conformations when incubated with 50 mM SDS. These anti-MRSA peptides could inhibit S. aureus and MRSA in concentrations of 2-32 μg/mL. P1 (NH₂-VVVNVLVKVLPPPVV-COOH) had the highest activity and was identified as a novel antimicrobial peptide (AMP). The stability study revealed that P1 was stable in response to temperature, proteolytic enzymes, surfactant, and pH. The electron micrograph showed that P1 induced bacterial membrane damage when treated at 1× MIC in the first hour of incubation. The killing kinetics of P1 was dependent on concentration and time. Mechanisms of P1 on tested pathogens involved membrane permeability, leakage of genetic material, and cell lysis. The P1 peptide at a concentration up to 32 μg/mL showed hemolysis of less than 10%, supporting its safety for human erythrocytes. This study provides promising anti-MRSA peptides that might be developed for effective antibiotics in the post-antibiotic era.

Molecular Characterization of an Intrinsically Disordered Chaperone Reveals Net-Charge Regulation in Chaperone Action

Molecular chaperones are diverse biomacromolecules involved in the maintenance of cellular protein homeostasis (proteostasis). Here we demonstrate that in contrast to most chaperones with defined three-dimensional structures, the acid-inducible protein Asr in Escherichia coli is intrinsically disordered and exhibits varied aggregation-preventing or aggregation-promoting activities, acting as a "conditionally active chaperone". Bioinformatics and experimental analyses of Asr showed that it is devoid of hydrophobic patches but rich in positive charges and local polyproline II backbone structures. Asr contributes to the integrity of the bacterial outer membrane under mildly acidic conditions in vivo and possesses chaperone activities toward model clients in vitro. Notably, its chaperone activity is dependent on the net charges of clients: on the one hand, it inhibits the aggregation of clients with similar net charges; on the other hand, it stimulates the aggregation of clients with opposite net charges. Mutational analysis confirmed that positively charged residues in Asr are essential for the varied effects on protein aggregation, suggesting that electrostatic interactions are the major driving forces underlying Asr's proteostasis-related activity. These findings present a unique example of an intrinsically disordered molecular chaperone with distinctive dual functions-as an aggregase or as a chaperone-depending on the net charges of clients.

Key Physicochemical Determinants in the Antimicrobial Peptide RiLK1 Promote Amphipathic Structures

Antimicrobial peptides (AMPs) represent a skilled class of new antibiotics, due to their broad range of activity, rapid killing, and low bacterial resistance. Many efforts have been made to discover AMPs with improved performances, i.e., high antimicrobial activity, low cytotoxicity against human cells, stability against proteolytic degradation, and low costs of production. In the design of new AMPs, several physicochemical features, such as hydrophobicity, net positive charge, propensity to assume amphipathic conformation, and self-assembling properties, must be considered. Starting from the sequence of the dodecapeptide 1018-K6, we designed a new 10-aminoacid peptide, namely RiLK1, which is highly effective against both fungi and Gram-positive and -negative bacteria at low micromolar concentrations without causing human cell cytotoxicity. In order to find the structural reasons explaining the improved performance of RiLK1 versus 1018-K6, a comparative analysis of the two peptides was carried out with a combination of CD, NMR, and fluorescence spectroscopies, while their self-assembling properties were analyzed by optical and atomic force microscopies. Interestingly, the different spectroscopic and microscopic profiles exhibited by the two peptides, including the propensity of RiLK1 to adopt helix arrangements in contrast to 1018-K6, could explain the improved bactericidal, antifungal, and anti-biofilm activities shown by the new peptide against a panel of food pathogens.

Computational Study of Helical and Helix-Hinge-Helix Conformations of an Anti-Microbial Peptide in Solution by Molecular Dynamics and Vibrational Analysis

Many classical antimicrobial peptides adopt an amphipathic helical structure at a water-membrane interface. Prior studies led to the hypothesis that a hinge near the middle of a helical peptide plays an important role in facilitating peptide-membrane interactions. Here, dynamics and vibrations of a designed hybrid antimicrobial peptide LM7-2 in solution were simulated to investigate its hinge formation. Molecular dynamics simulation results on the basis of the CHARMM36 force field showed that the α-helix LM7-2 bent around two or three residues near the middle of the peptide, stayed in a helix-hinge-helix conformation for a short period of time, and then returned to a helical conformation. High-resolution computational vibrational techniques were applied on the LM7-2 system when it has α-helical and helix-hinge-helix conformations to understand how this structural change affects its inherent vibrations. These studies concentrated on the calculation of frequencies that correspond to backbone amide bands I, II, and III: vibrational modes that are sensitive to changes in the secondary structure of peptides and proteins. To that end, Fourier transforms were applied to thermal fluctuations in C-N-H angles, C-N bond lengths, and C═O bond lengths of each amide group. In addition, instantaneous all-atom normal mode analysis was applied to monitor and detect the characteristic amide bands of each amide group within LM7-2 during the MD simulation. Computational vibrational results indicate that shapes and frequencies of amide bands II and especially III were altered only for amide groups near the hinge. These methods provide high-resolution vibrational information that can complement spectroscopic vibrational studies. They assist in interpreting spectra of similar systems and suggest a marker for the presence of the helix-hinge-helix motif. Moreover, radial distribution functions indicated an increase in the probability of hydrogen bonding between water and a hydrogen atom connected to nitrogen (HN) in such a hinge. The probability of intramolecular hydrogen bond formation between HN and an amide group oxygen atom within LM7-2 was lower around the hinge. No correlation has been found between the presence of a hinge and hydrogen bonds between amide group oxygen atoms and the hydrogen atoms of water molecules. This result suggests a mechanism for hinge formation wherein hydrogen bonds to oxygen atoms of water replace intramolecular hydrogen bonds as the peptide backbone folds.

UV Resonance Raman Structural Characterization of an (In)soluble Polyglutamine Peptide

Fibrillization of polyglutamine (polyQ) tracts in proteins is implicated in at least 10 neurodegenerative diseases. This generates great interest in the structure and the aggregation mechanism(s) of polyQ peptides. The fibrillization of polyQ is thought to result from the peptide's insolubility in aqueous solutions; longer polyQ tracts show decreased aqueous solution solubility, which is thought to lead to faster fibrillization kinetics. However, few studies have characterized the structure(s) of polyQ peptides with low solubility. In the work here, we use UV resonance Raman spectroscopy to examine the secondary structures, backbone hydrogen bonding, and side chain hydrogen bonding for a variety of solution-state, solid, and fibril forms of D₂Q₂₀K₂ (Q20). Q20 is insoluble in water and has a β-strand-like conformation with extensive inter- and intrapeptide hydrogen bonding in both dry and aqueous environments. We find that Q20 has weaker backbone-backbone and backbone-side chain hydrogen bonding and is less ordered compared to that of polyQ fibrils. Interestingly, we find that the insoluble Q20 will form fibrils when incubated in water at room temperature for ∼5 h. Also, Q20 can be prepared using a well-known disaggregation procedure to produce a water-soluble PPII-like conformation with negligible inter- and intrapeptide hydrogen bonding and a resistance to aggregation.

Ultraviolet Resonance Raman Spectroscopic Markers for Protein Structure and Dynamics

UV resonance Raman (UVRR) spectroscopy is a powerful tool for investigating the structure of biological molecules, such as proteins. Numerous UVRR spectroscopic markers that provide information on the structure and environment of the protein backbone and of amino acid side chains have recently been discovered. Combining these UVRR markers with hydrogen-deuterium exchange and advanced statistics is a powerful tool for studying protein systems, including the structure and formation mechanism of protein aggregates and amyloid fibrils. These techniques allow crucial new insights into the structure and dynamics of proteins, such as polyglutamine peptides, which are associated with 10 different neurodegenerative diseases. Here we summarize the spectroscopic structural markers recently developed and the important insights they provide.

Secondary structure and dynamics study of the intrinsically disordered silica-mineralizing peptide P5 S3 during silicic acid condensation and silica decondensation

The silica forming repeat R5 of sil1 from Cylindrotheca fusiformis was the blueprint for the design of P5 S3 , a 50-residue peptide which can be produced in large amounts by recombinant bacterial expression. It contains 5 protein kinase A target sites and is highly cationic due to 10 lysine and 10 arginine residues. In the presence of supersaturated orthosilicic acid P5 S3 enhances silica-formation whereas it retards the dissolution of amorphous silica (SiO2 ) at globally undersaturated concentrations. The secondary structure of P5 S3 during these 2 processes was studied by circular dichroism (CD) spectroscopy, complemented by nuclear magnetic resonance (NMR) spectroscopy of the peptide in the absence of silicate. The NMR studies of dual-labeled (13 C, 15 N) P5 S3 revealed a disordered structure at pH 2.8 and 4.5. Within the pH range of 4.5-9.5 in the absence of silicic acid, the CD data showed a disordered structure with the suggestion of some polyproline II character. Upon silicic acid polymerization and during dissolution of preformed silica, the CD spectrum of P5 S3 indicated partial transition into an α-helical conformation which was transient during silica-dissolution. The secondary structural changes observed for P5 S3 correlate with the presence of oligomeric/polymeric silicic acid, presumably due to P5 S3 -silica interactions. These P5 S3 -silica interactions appear, at least in part, ionic in nature since negatively charged dodecylsulfate caused similar perturbations to the P5 S3 CD spectrum as observed with silica, while uncharged ß-d-dodecyl maltoside did not affect the CD spectrum of P5 S3 . Thus, with an associated increase in α-helical character, P5 S3 influences both the condensation of silicic acid into silica and its decondensation back to silicic acid.

Glutamine and Asparagine Side Chain Hyperconjugation-Induced Structurally Sensitive Vibrations

We identified vibrational spectral marker bands that sensitively report on the side chain structures of glutamine (Gln) and asparagine (Asn). Density functional theory (DFT) calculations indicate that the Amide III(P) (AmIII(P)) vibrations of Gln and Asn depend cosinusoidally on their side chain OCCC dihedral angles (the χ3 and χ2 angles of Gln and Asn, respectively). We use UV resonance Raman (UVRR) and visible Raman spectroscopy to experimentally correlate the AmIII(P) Raman band frequency to the primary amide OCCC dihedral angle. The AmIII(P) structural sensitivity derives from the Gln (Asn) Cβ-Cγ (Cα-Cβ) stretching component of the vibration. The Cβ-Cγ (Cα-Cβ) bond length inversely correlates with the AmIII(P) band frequency. As the Cβ-Cγ (Cα-Cβ) bond length decreases, its stretching force constant increases, which results in an upshift in the AmIII(P) frequency. The Cβ-Cγ (Cα-Cβ) bond length dependence on the χ3 (χ2) dihedral angle results from hyperconjugation between the Cδ═Oϵ (Cγ═Oδ) π* and Cβ-Cγ (Cα-Cβ) σ orbitals. Using a Protein Data Bank library, we show that the χ3 and χ2 dihedral angles of Gln and Asn depend on the peptide backbone Ramachandran angles. We demonstrate that the inhomogeneously broadened AmIII(P) band line shapes can be used to calculate the χ3 and χ2 angle distributions of peptides. The spectral correlations determined in this study enable important new insights into protein structure in solution, and in Gln- and Asn-rich amyloid-like fibrils and prions.