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Samuel H Gellman

Publications and source records attributed to Samuel H Gellman.

At least 37 records · Page 2Linked to original sources
PubMed2005

Residue requirements for helical folding in short alpha/beta-peptides: crystallographic characterization of the 11-helix in an optimized sequence.

Design of functional foldamers requires knowledge of the conformational propensities of constituent residues. Here, we explore the effects of variations in both alpha-amino acid and beta-amino acid substitution on alpha/beta-peptide helicity. We also report the first X-ray crystal structure of a helical alpha/beta-peptide. We conclude that a certain amount of conformational preorganization in alpha/beta-peptides (via the inclusion of constrained beta-amino acids or alpha,alpha-disubstituted alpha-amino acids) is needed to promote helical folding; acyclic beta-amino acids and beta-branched alpha-amino acids are tolerated to only a limited extent.

Carbohydrate Sequence↗
PubMed2005

Chimeric (alpha/beta + alpha)-peptide ligands for the BH3-recognition cleft of Bcl-XL: critical role of the molecular scaffold in protein surface recognition.

Molecules that bind to specific surface sites on proteins are of great interest from both fundamental and practical perspectives. We are exploring a ligand development strategy that is based on oligomers with discrete folding propensities ("foldamers"); we target a specific cleft on the cancer-associated protein Bcl-xL because this system is well characterized structurally. In vivo, this cleft binds to alpha-helical segments (BH3 domains) of other proteins. We evaluated several types of helical foldamer, built entirely from beta-amino acid residues or from mixtures of alpha- and beta-amino acid residues, and ultimately identified foldamers in the latter class that bind very tightly to Bcl-xL. Our results suggest that combining different types of foldamer backbones will be an effective and general strategy for creating high-affinity and specific ligands for protein surface sites.

Binding, Competitive↗
PubMed2005

Enantioselective organocatalytic Michael additions of aldehydes to enones with imidazolidinones: cocatalyst effects and evidence for an enamine intermediate.

An enantioselective intermolecular Michael addition of aldehydes to enones catalyzed by imidazolidinones has been achieved. Chemoselectivity (Michael addition vs aldol) can be controlled through judicious choice of hydrogen-bond-donating cocatalysts. The optimal imidazolidinone/hydrogen-bond-donor pair affords Michael addition products in excess of 90% ee. Furthermore, we have isolated and characterized an enamine intermediate and demonstrated its efficacy as a nucleophile in the observed Michael addition reactions.

Aldehydes↗
PubMed2005

Use of parallel synthesis to probe structure-activity relationships among 12-helical beta-peptides: evidence of a limit on antimicrobial activity.

We report structure-activity trends among helix-forming beta-amino acid oligomers that are intended to mimic alpha-helical host-defense peptides. Parallel synthesis of two small, focused beta-peptide libraries allowed us to identify relatively short (11-residue) beta-peptides that display antimicrobial activity. These beta-peptides exhibit selectivity for bacteria relative to human red blood cells. A large hydrophobic helical surface is necessary for antimicrobial activity. Longer analogues (16 residues) of the most active library members were prepared and evaluated. Some of these longer beta-peptides showed very good antimicrobial activity, but none was more active than a previously reported beta-peptide [Porter, E. A.; Wang, X.; Lee, H.-S.; Weisblum, B.; Gellman, S. H. Nature 2000, 404, 565]. The extensive literature on alpha-helical host-defense peptides and related alpha-peptides indicates that such molecules are seldom active at concentrations below 1 microg/mL, and our results suggest that amphiphilic helical beta-peptides are subject to a comparable limit.

Amino Acid Sequence↗
PubMed2005

Crystallization of bacteriorhodopsin solubilized by a tripod amphiphile.

Bacteriorhodopsin (bR) is solubilized efficiently as a monomer by a novel surfactant, a tripod amphiphile (TPA), which permits the formation of purple hexagonal bR crystals under several conditions. The crystals, although small, diffract to 2.5 A resolution using synchrotron radiation. TPA may be useful for the solubilization, purification, and crystallization of other membrane proteins.

Bacteriorhodopsins↗
PubMed2005

A rapid 1H NMR assay for enantiomeric excess of alpha-substituted aldehydes.

In situ derivatization of a variety of alpha-substituted aldehydes via reaction with chiral amines allows convenient and efficient determination of enantiomeric excess. (1)H NMR analysis of the imine diastereomer ratio can be conducted immediately after the aldehyde and amine have been mixed. The results correlate well with ee values determined by more traditional (and slower) methods. This approach may be broadly applicable to alpha-substituted aldehydes. [reaction: see text]

Aldehydes↗
PubMed2005

Synthesis of 2,2-disubstituted pyrrolidine-4-carboxylic acid derivatives and their incorporation into beta-peptide oligomers.

[reaction: see text] We have recently shown that members of a new class of beta-peptides, containing 2,2-disubstituted pyrrolidine-4-carboxylic acid residues, display discrete conformational preferences despite the impossibility of internal hydrogen bonding (Huck et al. J. Am. Chem. Soc. 2003, 125, 9035). Here we describe the synthesis of a variety of 2,2-disubstituted pyrrolidine-4-carboxylic derivatives that bear a diverse set of side chains and protecting groups suitable for oligomer synthesis. In addition, we discuss coupling methods for construction of oligomers in solution and on solid phase. Non-hydrogen bonded foldamers such as those generated from 2,2-disubstituted pyrrolidine-4-carboxylic acids may be useful in biomedical applications because the low intrinsic polarity of their backbones may promote bioavailability.

Carboxylic Acids↗
PubMed2005

Application of microwave irradiation to the synthesis of 14-helical beta-peptides.

[structure: see text] We have evaluated the effects of microwave irradiation on the solid-phase synthesis of beta-peptides. Sequences designed to adopt the 14-helix, especially those containing the structure-promoting residue trans-2-aminocyclohexanecarboxylic acid (ACHC), suffer from poor synthetic efficiency under standard SPPS conditions. A comparison of microwave and conventional heating shows that both provide excellent synthetic results for shorter sequences; however, we identify a clear benefit from microwave irradiation for longer beta-peptides.

Combinatorial Chemistry Techniques↗
PubMed2005

Effects of conformational stability and geometry of guanidinium display on cell entry by beta-peptides.

We have used our ability to control beta-peptide secondary structure in order to explore the effects of conformational stability and geometry of guanidinium display on cell entry. Both of these factors affect the rate and relative amount of beta-peptide accumulation in the cytoplasm and nucleus of live HeLa cells. These beta-peptides do not show significant differences in cell surface binding, implying that structure and guanidinium display are important in a later step in cell entry than initial surface binding.

Arginine↗
PubMed2005

An autonomously folding beta-hairpin derived from the human YAP65 WW domain: attempts to define a minimum ligand-binding motif.

WW domains are broadly distributed among natural proteins; these modules play a role in bringing specific proteins together. The ligands recognized by WW domains are short segments rich in proline residues. We have tried to identify the minimum substructure within a WW domain that is required for ligand binding. WW domains typically comprise ca. 40 residues and fold to a three-stranded beta-sheet. Structural data for several WW domain/ligand complexes suggest that most or all of the intermolecular contacts involve beta-strands 2 and 3. We have developed a 16-residue peptide that folds to a beta-hairpin conformation that appears to mimic beta-strands 2 and 3 of the human YAP65 WW domain, but this peptide does not bind to known ligands. Thus, the minimum binding domain is larger than the latter two strands of the WW domain beta-sheet.

Adaptor Proteins, Signal Transducing↗
PubMed2004

Synthesis of 4,4-disubstituted 2-aminocyclopentanecarboxylic acid derivatives and their incorporation into 12-helical beta-peptides.

An enantioselective synthetic route is reported for trans-2-aminocyclopentanecarboxylic acids (ACPC) bearing geminal side chain pairs at the 4-position. Beta-peptides containing the 4,4-disubstituted ACPC residues adopt the 12-helical conformation, as demonstrated by 2D NMR analysis in aqueous solution. These 4,4-disubstituted ACPC residues display functional groups, including acidic and hydrogen bond donating groups, in a geometrically defined fashion, which should be useful for the design of beta-peptides for specific applications. [structure: see text]

Carboxylic Acids↗
PubMed2004

Backbone thioester exchange: a new approach to evaluating higher order structural stability in polypeptides.

An amide bond has been replaced by a thioester in bovine pancreatic polypeptide (bPP) to allow rapid and reversible (dynamic) exchange of the alpha-helical segment with other thiols in solution. We have begun to study the higher order structural stability of bPP by measuring the equilibrium constant of the "backbone thioester exchange" (BTE) reaction. The extent to which the equilibrium (KBTE) favors one set of peptides over the other, which can be easily measured, can be directly correlated to the energy gained from favorable noncovalent interactions that occur between peptide segments on either side of the thioester bond (Kfold).

Amino Acid Sequence↗
PubMed2004

Hydrophobic core repacking in a coiled-coil dimer via phage display: insights into plasticity and specificity at a protein-protein interface.

The coiled-coil, which consists of two or more interwoven amphiphilic alpha-helices, is formed by sequences that have a characteristic heptad repeat (abcdefg) where a and d are hydrophobic residues. Most efforts to elucidate the origins of coiled-coil pairing selectivity have focused on electrostatic interactions among side chains that flank the core (positions e and g) and on polar side chains that occur occasionally at core positions. We have used phage display to explore another source of coiled-coil specificity: steric matching among nonpolar side chains in the core. We introduced a destabilizing Leu-->Ala mutation into the core of one helix in a known heterodimer and then screened a phage-based library of potential partner helices in search of compensating mutations. We identified a new heterodimer pair (30 residues/helix) that is comparable in stability to the GCN4-p1 homodimer (33 residues/helix). Furthermore, the Leu-->Ala mutant shows specificity for its phage-derived partner over the original partner despite their similar sequences. These results show that a phage-based approach can provide unique insights on coiled-coil pairing preferences that should facilitate both the analysis of natural sequences and the development of specific dimerization motifs that are orthogonal to one another.

Alanine↗
PubMed2004

Antimicrobial 14-helical beta-peptides: potent bilayer disrupting agents.

The interactions of two amphiphilic and cationic, nine-residue beta-peptides with liposomal membranes were studied. These beta-peptides are shown to form 14-helices in the presence of bilayers. Membrane binding and membrane permeabilization occur preferentially in the presence of anionic lipids. The beta-peptides have the ability to cause tranbilayer diffusion of phospholipids, form pores, and promote lipid mixing between liposomes. These beta-peptides have previously been shown to display antimicrobial activity comparable to that of a longer beta-peptide, beta-17, which adopts a different type of helical conformation (12-helix), and to the 23 amino acid (Ala(8,13,18))-magainin-II-amide, which adopts an alpha-helical conformation. In addition, these 14-helical beta-peptides show relatively low hemolytic activity. The biological potency and microbial specificity of the 14-helical beta-peptides, despite their relatively short length, suggests that 14-helices can be particularly disruptive to microbial membranes.

Amino Acid Sequence↗
PubMed2004

Unexpected relationships between structure and function in alpha,beta-peptides: antimicrobial foldamers with heterogeneous backbones.

We describe our first effort to design antimicrobial alpha/beta-peptides based upon their helical folding behavior. alpha/beta-Peptide 3 (above), designed as a scrambled negative control, exhibited the most favorable activity profile, combining high antimicrobial activity with low hemolytic activity. This finding suggests that design principles focused primarily on structures that adopt globally amphiphilic structures may exclude productive possibilities from evaluation.

Anti-Bacterial Agents↗
PubMed2004

Effects of alternative side chain pairings and reverse turn sequences on antiparallel sheet structure in beta-peptide hairpins.

[structure: see text] We describe a series of beta-peptide hexamers that allow us to explore relationships between sequence and hairpin folding. Different reverse turn segments are compared at the central two positions, and the outer residues allow a variety of interstrand side chain-side chain pairings. NMR analysis in methanol demonstrates that several reverse turn and side chain pairing arrangements are compatible with antiparallel beta-peptide sheet structure; however, none of the beta-peptides folds in water.

Magnetic Resonance Spectroscopy↗
PubMed2004

Biocidal activity of polystyrenes that are cationic by virtue of protonation.

[structure: see text] Poly(1) kills bacteria (Gram-positive and -negative) and lyses human erythrocytes; this biocidal profile is similar to that of the peptide toxin mellitin. Poly(1) has antibacterial activity comparable to that of a potent derivative of the host defense peptide magainin II, but lacks magainin's selectivity for bacteria over erythrocytes. An analogous N-quaternized polymer, poly(3), is less biocidal than poly(1), suggesting that reversible N-protonation leads to greater biocidal activity than does irreversible N-quaternization.

Anti-Bacterial Agents↗