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Marcey L Waters

Publications and source records attributed to Marcey L Waters.

At least 19 recordsLinked to original sources
PubMed2006

Pressure perturbation calorimetry of helical peptides.

Pressure perturbation calorimetry quantifies the temperature dependence of a solute's thermal expansion coefficient, providing information about solute-solvent interactions. We tested the idea that pressure perturbation calorimetry can provide information about solvent-accessible surface area by studying peptides with different secondary structures. The peptides comprised two host-guest series: one predominately an alpha-helix, the other predominately a polyproline II helix. In aqueous buffer, we find a correlation between the amount of secondary structure as assessed by circular dichroism spectropolarimetry and the pressure perturbation calorimetry data. We conclude that pressure perturbation calorimetry can provide information about the exposure of polar and nonpolar surface area. Data acquired in a buffered urea solution, however, are not as easily interpreted.

Calorimetry↗
PubMed2005

Molecular recognition with designed peptides and proteins.

The design of proteins and peptides as molecular receptors is a rapidly growing area of research. Two primary approaches have been utilized, involving the minimization of known protein binding motifs or the de novo design of binding pockets within well-folded protein structures. These approaches are complementary and help define the minimum requirements necessary for biomolecular recognition. Recent advances in this area include the design of cavities within helix bundles for the binding of anesthetics, the design of beta-hairpins for the recognition of nucleotides and oligonucleotides, the redesign of protein binding sites for unique ligands, and the design of mini-proteins via protein grafting for the recognition of proteins and DNA. These advances provide exciting new opportunities to develop novel biosensors, de novo designed catalysts, exogenously triggered synthetic signal transduction cascades, and novel approaches to therapeutic treatments.

Models, Molecular↗
PubMed2005

Turn residues in beta-hairpin peptides as points for covalent modification.

Beta-turns are important sites for protein-protein and protein-peptide interactions, but little research has explored synthetic modifications of turn residue side-chains in a beta-hairpin peptide. To this end, beta-hairpin peptides were synthesized containing the type I' turn sequence Val-Asn-Gly-Lys with modifications at Asn and Lys. We found that these variations impose a small penalty, demonstrating that beta-turns are capable of displaying a range of functionality, which may be exploited for biomolecular recognition and medicinal applications. [structure: see text]

Amino Acid Sequence↗
PubMed2005

Influence of N-methylation on a cation-pi interaction produces a remarkably stable beta-hairpin peptide.

The methylation of lysine in histone tails is a common posttranslational modification that functions in histone-regulated chromatin condensation, with binding of methylated lysine occurring in aromatic pockets on chromodomain proteins. We have synthesized a highly stable 12-residue beta-hairpin peptide that exploits the histone-related cation-pi interaction between a methylated lysine residue and a tryptophan residue. Thermodynamic analysis reveals significant entropic stabilization of the peptide due to methylation of the lysine residue. Chemical denaturation of the peptide demonstrates two-state behavior. In comparison to other reported, highly stable designed beta-hairpins, this peptide is the most thermally stable beta-hairpin reported to date. This study provides insight into the role of Lys methylation in histone proteins and more generally in mediating protein-protein interactions.

Amino Acid Sequence↗
PubMed2005

The recognition of nucleotides with model beta-hairpin receptors: investigation of critical contacts and nucleotide selectivity.

[reaction: see text] We have investigated the factors that contribute to binding of ATP by a designed 12-residue beta-hairpin peptide, WKWK, and have determined its selectivity for binding to the naturally occurring nucleotide triphosphates. We have previously shown that WKWK creates an ATP binding pocket on one face of the beta-hairpin consisting of two Trp and two Lys residues. Mutation of the two Lys residues on the binding face of the beta-hairpin resulted in a lower affinity, indicating that each is involved in ATP binding and that each residue contributes approximately -1.5 kcal/mol to the energy of complexation. Replacement of either Trp residue of the ATP binding pocket with Phe or Leu destabilizes the complex formed with ATP by approximately 1 kcal/mol, indicating that both Trp residues participate in interactions with ATP. For binding to the nucleotide triphosphates, the order of binding affinity was shown to follow dTTP > GTP > ATP > CTP, with differences in binding energies spanning as much as 1.6 kcal/mol. NMR analysis demonstrates that both aromatic interactions with the Trp side chains and CH-pi interactions between the ribose protons and the Trp residues may contribute significantly to binding. The results from our model system provide useful thermodynamic information regarding protein-nucleic acid interactions that occur at the surface of a beta-sheet.

Amino Acid Sequence↗
PubMed2005

Minimalist protein design: a beta-hairpin peptide that binds ssDNA.

A 28-residue beta-hairpin dimer (WKWK)2 with two Trp and two Lys residues on one face of each beta-sheet was shown to form a complex with single-stranded oligonucleotides at low micromolar concentrations. Each beta-hairpin of the dimer contains a cross-strand Trp-Trp pair in a diagonal orientation which has previously been shown to create a cleft for the intercalation of aromatic guests such as adenine (J. Am. Chem. Soc. 2003, 125, 9580). The beta-hairpin dimer binds 5-residue ssDNA sequences 5'-AAAAA-3', 5'-TTTTT-3', and 5'-CCCCC-3' in water with dissociation constants in the range of 12-30 muM. A weak energetic preference for binding to sequence 5'-AAAAA-3' was observed, which is believed to result from stronger stacking interactions between Trp and the adenine base. The interaction of 5'-AAAAA-3' with the Lys and Trp residues of the peptide was evident by NMR, and a 1:1 association was demonstrated. The recognition of an 11-residue ssDNA sequence occurred with a dissociation constant of 3 muM under near-physiological ionic strength and pH, demonstrating that the beta-hairpin dimer binds ssDNA as strongly as many naturally occurring proteins. The salt dependence of the interaction of the 11-residue oligonucleotide with the peptide dimer indicates that Trp-nucleobase stacking interactions contribute about -4 kcal/mol to recognition, which is much greater than the contribution of nonionic interactions in unstructured peptides containing Trp. Moreover, recognition of the ssDNA demonstrated reduced salt dependence relative to the corresponding duplex, resulting in selectivity for ssDNA under high salt conditions. Peptide (WKWK)2 is a relevant mimic of OB-fold (oligonucleotide/oligosaccharide-binding) proteins which bind ssDNA on the surface of a beta-sheet.

DNA, Single-Stranded↗
PubMed2004

Effect of halogenation on edge-face aromatic interactions in a beta-hairpin peptide: enhanced affinity with iodo-substituents.

[reaction: see text] In a model beta-hairpin peptide, we have found that the favorable interaction of cross-strand aromatic rings can be enhanced by up to 1 kcal mol(-1) with halogen substituents. It appears that the polarizability of the halogen atoms accounts for the increase in stability and that there is a direct interaction between the N-terminal phenylalanine and the halogen atom. Thermal denaturation studies indicate that the interaction is enthalpically driven with an associated entropic cost. These findings have relevance to areas of molecular recognition and drug design.

Amino Acid Sequence↗
PubMed2004

Orientation and alkylation effects on cation-pi interactions in aqueous solution.

We have investigated the orientation dependence of the cation-pi interaction between a phenyl ring and a pyridinium ring in the context of a flexible model system in water. Of the four possible positions of the pyridinium nitrogen, ipso, ortho, meta, and para, we found a variation in the interaction energy of about 0.75 kcal mol(-1), with the stacking of the ipso-pyridinium ring providing the strongest interaction. The observed stability is attributed to the maximization of the electrostatic interaction, minimization of rotamers, and possible differences in hydration phenomena arising from alkylation.

Journal Article↗
PubMed2004

Comparison of C-H...pi and hydrophobic interactions in a beta-hairpin peptide: impact on stability and specificity.

We have examined the impact of C-H...pi and hydrophobic interactions in the diagonal position of a beta-hairpin peptide through comparison of the interaction of Phe, Trp, or Cha (cyclohexylalanine) with Lys or Nle (norleucine). NMR studies, including NOESY and chemical shift perturbation studies, of the Lys side chain indicates that Lys interacts in a specific geometry with Phe or Trp through the polarized C epsilon. In contrast, Nle does not interact in a specific manner with the diagonal aromatic residue. Thermal denaturation provides additional support that Lys and Nle interact in fundamentally different manners. Folding of the peptide with a diagonal Trp...Lys interaction was found to be enthalpically driven, whereas the peptide with a diagonal Trp...Nle interaction displayed cold denaturation, as did the control peptide with a diagonal Cha...Nle interaction, indicating different driving forces for interaction of Lys and Nle with Trp. These findings have significant implications for specificity in protein folding and de novo protein design.

Anisotropy↗
PubMed2004

Aromatic interactions in peptides: impact on structure and function.

Aromatic interactions, including pi-pi, cation-pi, aryl-sulfur, and carbohydrate-pi interactions, have been shown to be prevalent in proteins through protein structure analysis, suggesting that they are important contributors to protein structure. However, the magnitude and significance of aromatic interactions is not defined by such studies. Investigation of aromatic interactions in the context of structured peptides has complemented studies of protein structure and has provided a wealth of information regarding the role of aromatic interactions in protein structure and function. Recent advances in this area are reviewed.

Amino Acids, Aromatic↗
PubMed2004

Investigation of the nature of the methionine-pi interaction in beta-hairpin peptide model systems.

There are frequent contacts between aromatic rings and sulfur atoms in proteins. However, it is unclear to what degree this putative interaction is stabilizing and what the nature of the interaction is. We have investigated the aryl-sulfur interaction by placing a methionine residue diagonal to an aromatic ring on the same face of a beta-hairpin, which places the methionine side chain in close proximity to the aryl side chain. The methionine (Met)-aryl interaction was compared with an equivalent hydrophobic and cation-pi interaction in the context of the beta-hairpin. The interaction between phenylalanine (Phe), tryptophan (Trp), or cyclohexylalanine (Cha) and Met stabilized the beta-hairpin by -0.3 to -0.5 kcal mole(-1), as determined by double-mutant cycles. The peptides were subjected to thermal denaturations that suggest a hydrophobic driving force for the interactions between Met and Trp or Cha. The observed interaction of Met or norleucine (Nle) with Trp or Cha are quite similar, implying a hydrophobic driving force for the Met-pi interaction. However, the thermodynamic data suggest that there may be some differences between the interaction of Met with Trp and Phe and that there may be a small thermodynamic component to the Met...Phe interaction.

Amides↗
PubMed2003

A designed beta-hairpin peptide for molecular recognition of ATP in water.

A designed 12-residue beta-hairpin peptide with a diagonal tryptophan (Trp) pair was shown to bind ATP in water through a combination of aromatic and electrostatic interactions. The affinity for ATP was 5800 M-1 (DeltaG approximately -5.0 kcal/mol), a remarkable affinity for a short, structured peptide in water, consisting of entirely natural amino acid residues. Proton NMR measurements indicate that the adenine ring of the nucleotide is intercalated between the diagonal tryptophans in the bound state. Delineation of the contributions to ATP binding to the hairpin suggest that aromatic interactions contribute approximately -1.8 kcal/mol, while individual electrostatic interactions involving the ATP phosphates and positively charged side chains of the hairpin contribute approximately -1 kcal/mol each. The designed beta-hairpin receptor presents a novel minimalist system to investigate the energetic contributions to protein-nucleic acid recognition through the surface of a beta-sheet.

Adenosine Triphosphate↗
PubMed2003

Sequence dependence of beta-hairpin structure: comparison of a salt bridge and an aromatic interaction.

A comparison of the contributions and position dependence of cross-strand electrostatic and aromatic side-chain interactions to beta-sheet stability has been performed by using nuclear magnetic resonance in a well-folded beta-hairpin peptide of the general sequence XRTVXVdPGOXITQX. Phe-Phe and Glu-Lys pairs were varied at the internal and terminal non-hydrogen-bonded position, and the resulting stability was measured by the effects on alpha-hydrogen and aromatic hydrogen chemical shifts. It was determined that the introduction of a Phe-Phe pair resulted in a more folded peptide, regardless of position, and a more tightly folded core. Substitution of the Glu-Lys pair at the internal position results in a less folded peptide and increased fraying at the terminal residues. Upfield shifting of the aromatic hydrogens provided evidence for an edge-face aromatic interaction, regardless of position of the Phe-Phe pair. In peptides with two Phe-Phe pairs, substitution with Glu-Lys at either position resulted in a weakening of the aromatic interaction and a subsequent decrease in peptide stability. Thermal denaturation of the peptides containing Phe-Phe indicates that the aromatic interaction is enthalpically favored, whereas the folding of hairpins with cross-strand Glu-Lys pairs was less enthalpically favorable but entropically more favorable.

Amino Acid Sequence↗
PubMed2003

The geometry and efficacy of cation-pi interactions in a diagonal position of a designed beta-hairpin.

Cation-pi interactions are common in proteins, but their contribution to the stability and specificity of protein structure has not been well established. In this study, we examined the impact of cation-pi interactions in a diagonal position of a beta-hairpin peptide through comparison of the interaction of Phe or Trp with Lys or Arg. The diagonal interactions ranged from -0.20 to -0.48 kcal/mole. Our experimental values for the diagonal cation-pi interactions are similar to those found in alpha-helical studies. Upfield shifting of the Lys and Arg side chains indicates that the geometries of cation-pi interactions adopted in the 12-residue beta-hairpin are comparable to those found in protein structures. The Lys was found to interact through the polarized Cepsilon, and the Arg is stacked against the aromatic ring of Phe or Trp. Folding of these peptides was found to be enthalpically favorable (DeltaH degrees equals approximately -3 kcal/mole) and entropically unfavorable (DeltaS degrees equals approximately -8 cal mole(-1) K(-1)).

Arginine↗
PubMed2002

Simple cation-pi interaction between a phenyl ring and a protonated amine stabilizes an alpha-helix in water.

Cation-pi interactions have been proposed to be important contributors to protein structure and function. In particular, these interactions have been suggested to provide significant stability at the solvent-exposed surface of a protein. We have investigated the magnitude of cation-pi interactions between phenylalanine (Phe) and lysine (Lys), ornithine (Orn), and diaminobutanoic acid (Dab) in the context of an alpha-helix and have found that only the Phe...Orn interaction provides significant stability to the helix, stabilizing it by -0.4 kcal/mol. This interaction energy is in the same range as a salt bridge in an alpha-helix, and equivalent to the recently reported Trp...Arg interaction in an alpha-helix, despite the fact that Trp...guanidinium interactions have been proposed to be stronger than Phe...ammonium interactions. These results indicate that even the simplest cation-pi interaction can provide significant stability to protein structure and demonstrate the subtle factors that can influence the observed interaction energies in designed systems.

Amino Acid Sequence↗
PubMed2002

Contribution of aromatic interactions to alpha-helix stability.

The influence of natural and unnatural i, i + 4 aromatic side chain-side chain interactions on alpha-helix stability was determined in Ala-Lys host peptides by circular dichroism (CD). All interactions investigated provided some stability to the helix; however, phenylalanine-phenylalanine (F-F) and phenylalanine-pentafluorophenylalanine (F-f5F) interactions resulted in the greatest enhancement in helicity, doubling the helical content over i, i + 5 control peptides at internal positions. Quantification of these interactions using AGADIR multistate helix-coil algorithm revealed that the F-F and F-f5F interaction energies are equivalent at internal positions in the sequence (deltaGF-F = deltaGF-f5F = -0.27 kcal/mol), despite the differences in their expected geometries. As the strength of a face-to-face stacked phenyl-pentafluorophenyl interaction should surpass an edge-to-face or offset-stacked phenyl-phenyl interaction, we believe this result reflects the inability of the side chains in F-f5F to attain a fully stacked geometry within the context of an alpha-helix. Positioning the interactions at the C-terminus led to much stronger interactions (deltaGF-F = -0.8 kcal/mol; deltaGF-f5F = -0.55 kcal/mol) likely because of favorable chi(1) rotameric preferences for aromatic residues at C-capping regions of alpha-helices, suggesting that aromatic side chain-side chain interactions are an effective alpha-helix C-capping method.

Alanine↗
PubMed2002

Selective aromatic interactions in beta-hairpin peptides.

To probe the selectivity possible in hydrophobic clusters, we have compared the cross-strand interactions of phenylalanine (Phe) and cyclohexylalanine (Cha) in a beta-hairpin peptide. We have found a preference for self-association among the aromatic residues, which provides 0.55 kcal/mol in stability relative to Cha-Cha cross-strand pair. NMR analysis of the Phe-Phe cross-strand pair indicates that it interacts in an edge-face interaction, despite the fact that it is highly solvent-exposed. The interaction geometry as well as the enthalpic and entropic values for the peptide containing the Phe-Phe cross-strand pair suggest that the preference for self-association arises from inherent differences in the nature of aromatic and aliphatic interactions in water.

Peptides↗