The bacterial cell surface

Water-medicated specifically targeting the S1 pockets among serine proteases using an arginine analogue

Because of the high similarity in structure and sequence, it is challenging to distinguish the S1 pocket among serine proteases, primarily due to the only variability at residue 190 (A190 and S190). Peptide or protein-based inhibitors typically target the negatively charged S1 pocket using lysine or arginine as the P1 residue, yet neither discriminates between the two S1 pocket variants. This study introduces two arginine analogues, L-4-guanidinophenylalanine (12) and L-3-(N-amidino-4-piperidyl)alanine (16), as novel P1 residues in peptide inhibitors. 16 notably enhances affinities across all tested proteases, whereas 12 specifically improved affinities towards proteases possessing S190 in the S1 pocket. By crystallography and molecular dynamics simulations, we discovered a novel mechanism involving a water exchange channel at the bottom of the S1 pocket, modulated by the variation of residue 190. Additionally, the specificity of 12 towards the S190-presenting S1 pocket is dependent on this water channel. This study not only introduces novel P1 residues to engineer inhibitory potency and specificity of peptide inhibitors targeting serine proteases, but also unveils a water-mediated molecular mechanism of targeting serine proteases.

Surface decoration with leucine tetrapeptide: An antibacterial strategy against Gram-negative bacteria

Surface-associated microbe contamination by Gram-negative bacteria poses a serious problem in medical care. Cationic peptides or polymers are the main materials used for antibacterial surface coating, but the positive charge may lead to blood coagulation. Therefore, exploiting surface coating which is free of positive charge and is effective for Gram-negative bacteria inactivation is in urgent need. In this study, inspired by the affinity between lipopolysaccharides of Gram-negative bacteria and Toll-like receptors of immune cells, we develop a leucine-based tetrapeptide coating strategy for combating Gram-negative bacteria. The obtained surface has excellent bactericidal activity against Gram-negative bacteria like Pseudomonas aeruginosa and Escherichia coli. A 1 mm² coated glass surface could kill > 9.9 × 10⁴ CFU bacteria in 1 h and has nearly no damage to mammal cells. Moreover, this surface coating strategy could be applied on various surfaces like glass slices, glass capillary cavity and thermoplastic polyurethane slices. And the coated surface could largely mitigate the microbe contamination in an in vivo subcutaneous implantation. This work paves a new way for antibacterial surface-coating which is behaving no positive charge and is of great importance for biomedical devices.

Stimulation of adenosine 5'-triphosphate-dependent in vitro deoxyribonucleic acid replication by factors from the periplasmic space of Escherichia coli

In vitro deoxyribonucleic acid (DNA) synthesis systems based on an earlier system using pencillin have been developed which use osmotic lysis of lysozyme-formed spheroplasts of Escherichia coli cells embedded in an agarose matrix. An adenosine 5'-triphosphate (ATP)-dependent semiconservative mode, or replicative mode, of in vitro DNA synthesis is exhibited which is sensitivie to nalidixic acid. These systems require growth of the agar-embedded cells in a preincubation medium before spheroplast formation and osmotic lysis. Inhibitor studies suggest that one or more required macromolecular species are synthesized during this preincubation growth period. Osmotic shock fluid from E. coli contains macromolecular factors which preferentially stimulate the ATP- dependent semiconservative mode of in vitro DNA synthesis. In some cases, the ATP independent mode of synthesis is inhibited by shock fluid. Evidence is presented that the stimulating factors found in the osmotic shock fluid come from the E. coli periplasmic space. This stimulation is observed using either toluene-treated cells or lysed agar-embedded ethylene glycol-bis-(beta-aminoethyl ether) N,N'-tetraacetate-lysozyme spheroplasts, and is thus independent of the in vitro DNA synthesis system used. Shock fluid obtained from a given E. coli dna mutant does not stimulate in vitro DNA synthesis by that mutant. However, in some cases, shock fluid from one class of dna mutants does stimulate ATP dependent in vitro DNA synthesis by another class of dna mutants, in a thermosensitive reacaction. Gently prepared cell extracts also stimulate ATP-dependent in vitro DNA synthesis, whereas cell extracts prepared by more severe procedures inhibit this in vitro synthesis. Severl stimulating DNA replication factors may be present in the osmotic shock fluid, including products of E. coli dna genes.