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Protein folding research often finds complex kinetic behavior which shows that unfolded molecules take several stages to convert to the fully native form. A Pro- variate of SNase's unfolding and folding kinetic mechanism was characterized using stopped-flow fluorescence methods, with alanines and glycines used in place of six proline residues. The folding kinetics still demonstrate a complex denaturant dependence, even though complicating factors such as prolines have been removed. A sequential four-state folding mechanism can be used to model the primary stages in unfolding and folding.

Individual protein domains and two domains in combination were prepared by enzymatic and chemical cleavage of turkey ovomucoid followed by isolation and purification by size-exclusion and ion-exchange chromatography. Silica bonded-phase HPLC columns were made from either whole or isolated domains of turkey ovomucoid. The protein columns were tested for chiral recognition by their abilities to resolve enantiomers among a wide range of racemates. The columns made from whole turkey ovomucoid displayed chiral activity toward many racemates, where as a combination of the first and second domain resolved only a selected number of aromatic weak bases. The first and second domains independently gave no appreciable chiral activity. The turkey ovomucoid third domain exhibited enantioselective protein binding for fused-ring aromatic weak acids. Glycosylation of the third domain did not affect chiral recognition. Titration of the third domain with model compounds in conjunction with NMR measurements enabled the identification of the amino acids responsible for binding. Molecular modeling of the ligand-protein complexation provided insights into the ability of a protein surface to discriminate enantiomers on the basis of multiple intermolecular interactions.

The backbone 1H and 15N resonances of unligated staphylococcal nuclease H124L were assigned by three-dimensional (3D) 1H-15N nuclear Overhauser- multiple-quantum coherence (NOESY-HMQC) nuclear magnetic resonance spectroscopy. Secondary structural elements (alpha-helices, beta-sheets, reverse turns and loops) were determined by analysis of patterns of NOE connectivities present in the 3D spectrum.

The biological activity of the selected peptides from the combinatorial library in bacteria, fungi and mammalian cells is studied to characterize the selected peptides and to compare the activity of antimicrobial peptides (AMPs) in vitro and in vivo. The analysis has shown that the methods focusing on screening peptide libraries in vitro for membranes with the appropriate interfacial activity has enabled the design, selection and discovery of novel, potent and broad-spectrum membrane-active antibiotics.

Pulsed hydrogen exchange methods were used to follow the formation of structure during the refolding of acid-denatured staphylococcal nuclease containing a stabilizing Leu substitution at position 124 (H124L SNase). The protection of more than 60 backbone amide protons in uniformly 15N-labeled H124L SNase was monitored as a function of refolding time by heteronuclear two-dimensional NMR spectroscopy. As found in previous studies of staphylococcal nuclease, partial protection was observed for a subset of amide protons even at the earliest folding time point (10 msec). Protection indicative of marginally stable hydrogen-bonded structure in an early folding intermediate was observed at over 30 amide positions located primarily in the β-barrel and to a lesser degree in the α-helical domain of H124L SNase. To further characterize the folding intermediate, protection factors for individual amide sites were measured by varying the pH of the labeling pulse at a fixed refolding time of 16 msec. Protection factors >5.0 were observed only for amide positions in a β-hairpin formed by strands 2 and 3 of the β-barrel domain and a single site near the C-terminus. The results indicate that formation of stable hydrogen-bonded structure in a core region of the β-sheet is among the earliest structural events in the folding of SNase and may serve as a nucleation site for further structure formation. [ABSTRACT FROM AUTHOR]

We recently described a family of cationic antimicrobial peptides (CAMPs) selected from a combinatorial library that exhibited potent, broad-spectrum activity at neutral pH and low ionic strength. To further delimit the utility and activity profiles of these peptides, we investigated the effects of solution conditions, such as pH and ionic strength, on the efficacy of the peptide antimicrobials against a panel of microorganisms. Peptide minimum sterilizing concentrations (MSCs) varied linearly with pH for each subtype within our family of CAMPs for all organisms tested. The peptides were much less effective against Gram-negative bacteria at high pH, consistent with a decrease in net positive charge on the peptides. A similar trend was observed for the fungus Candida albicans. Surprisingly, the opposite pH trend was observed with the Gram-positive Staphylococcus aureus. In addition, an additive ionic strength effect was observed with increasing buffer strengths at identical pH values. The extreme difference in the observed pH behavior between Gram-negative and Gram-positive organisms is attributed to the presence of native charged molecules in the much thicker peptidoglycan layer of the Gram-positive organism. The novel species-specific effects of pH observed here have important implications for applications using CAMPs and for the design of novel CAMPs.

Pulsed hydrogen exchange methods were used to follow the formation of structure during the refolding of acid-denatured staphylococcal nuclease containing a stabilizing Leu substitution at position 124 (H124L SNase). The protection of more than 60 backbone amide protons in uniformly (15)N-labeled H124L SNase was monitored as a function of refolding time by heteronuclear two-dimensional NMR spectroscopy. As found in previous studies of staphylococcal nuclease, partial protection was observed for a subset of amide protons even at the earliest folding time point (10 msec). Protection indicative of marginally stable hydrogen-bonded structure in an early folding intermediate was observed at over 30 amide positions located primarily in the beta-barrel and to a lesser degree in the alpha-helical domain of H124L SNase. To further characterize the folding intermediate, protection factors for individual amide sites were measured by varying the pH of the labeling pulse at a fixed refolding time of 16 msec. Protection factors >5.0 were observed only for amide positions in a beta-hairpin formed by strands 2 and 3 of the beta-barrel domain and a single site near the C-terminus. The results indicate that formation of stable hydrogen-bonded structure in a core region of the beta-sheet is among the earliest structural events in the folding of SNase and may serve as a nucleation site for further structure formation.