Stabilizing and destabilizing effects of phenylalanine --> F5-phenylalanine mutations on the folding of a small protein

We report a systematic evaluation of phenylalanine-to-pentafluorophenylalanine (Phe --> F5-Phe) mutants for the 35-residue chicken villin headpiece subdomain (c-VHP), the hydrophobic core of which features a cluster of three Phe side chains (residues 6, 10, and 17). Phe --> F5-Phe mutations are interesting because aryl-perfluoroaryl interactions of optimal geometry are intrinsically more favorable than aryl-aryl interactions and because perfluoroaryl units are more hydrophobic than are analogous aryl units. One mutant, Phe-10 --> F5-Phe, provides enhanced tertiary structural stability relative to the native sequence. The other six mutants analyzed caused a decrease in stability.     

Mechanism of Al(III)-catalyzed transamidation of unactivated secondary carboxamides

The carbon-nitrogen bond of secondary carboxamides is generally thermodynamically and kinetically unreactive; however, we recently discovered that the trisamidoaluminum(III) dimer Al2(NMe2)6 catalyzes facile transamidation between simple secondary carboxamides and primary amines under moderate conditions. The present report describes kinetic and spectroscopic studies that illuminate the mechanism of this unusual transformation. The catalytic reaction exhibits a bimolecular rate law with a first-order dependence on the Al(III) and amine concentrations. No rate dependence on the carboxamide concentration is observed. Spectroscopic studies (1H and 13C NMR, FTIR) support a catalyst resting state that consists of a mixture of tris-(kappa2-amidate)aluminum(III) complexes. These results, together with the presence of a significant kinetic isotope effect when deuterated amine substrate (RND2) is used, implicate a mechanism in which the amine undergoes preequilibrium coordination to aluminum and proton transfer to a kappa2-amidate ligand to yield an Al(kappa2-amidate)2(kappa1-carboxamide)(NHR) complex, followed by rate-limiting intramolecular delivery of the amido ligand (NHR) to the neutral Al(III)-activated kappa1-carboxamide. Noteworthy in this mechanism is the bifunctional character of Al(III), which is capable of activating both the amine nucleophile and the carboxamide electrophile in the reaction.     

The d'--d--d' vertical triad is less discriminating than the a'--a--a' vertical triad in the antiparallel coiled-coil dimer motif

Elucidating relationships between the amino-acid sequences of proteins and their three-dimensional structures, and uncovering non-covalent interactions that underlie polypeptide folding, are major goals in protein science. One approach toward these goals is to study interactions between selected residues, or among constellations of residues, in small folding motifs. The α-helical coiled coil has served as a platform for such studies because this folding unit is relatively simple in terms of both sequence and structure. Amino acid side chains at the helix-helix interface of a coiled coil participate in so-called "knobs-into-holes" (KIH) packing whereby a side chain (the knob) on one helix inserts into a space (the hole) generated by four side chains on a partner helix. The vast majority of sequence-stability studies on coiled-coil dimers have focused on lateral interactions within these KIH arrangements, for example, between an a position on one helix and an a' position of the partner in a parallel coiled-coil dimer, or between a--d' pairs in an antiparallel dimer. More recently, it has been shown that vertical triads (specifically, a'--a--a' triads) in antiparallel dimers exert a significant impact on pairing preferences. This observation provides impetus for analysis of other complex networks of side-chain interactions at the helix-helix interface. Here, we describe a combination of experimental and bioinformatics studies that show that d'--d--d' triads have much less impact on pairing preference than do a'--a--a' triads in a small, designed antiparallel coiled-coil dimer. However, the influence of the d'--d--d' triad depends on the lateral a'--d interaction. Taken together, these results strengthen the emerging understanding that simple pairwise interactions are not sufficient to describe side-chain interactions and overall stability in antiparallel coiled-coil dimers; higher-order interactions must be considered as well.     

Spherically symmetric inhomogeneous dust collapse in higher dimensional space-time and cosmic censorship hypothesis

We consider a collapsing spherically symmetric inhomogeneous dust cloud in higher dimensional space-time. We show that the central singularity of collapse can be a strong curvature or a weak curvature naked singularity depending on the initial density distribution.     

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.     

Interstrand side chain--side chain interactions in a designed beta-hairpin: significance of both lateral and diagonal pairings

The contributions of interstrand side chain-side chain contacts to beta-sheet stability have been examined with an autonomously folding beta-hairpin model system. RYVEV(D)PGOKILQ-NH2 ((D)P = D-proline, O = ornithine) has previously been shown to adopt a beta-hairpin conformation in aqueous solution, with a two-residue loop at D-Pro-Gly. In the present study, side chains that display interstrand NOEs (Tyr-2, Lys-9, and Leu-11) are mutated to alanine or serine, and the conformational impact of the mutations is assessed. In the beta-hairpin conformation Tyr-2 and Leu-11 are directly across from one another (non-hydrogen bonded pair). This "lateral" juxtaposition of two hydrophobic side chains appears to contribute to beta-hairpin conformational stability, which is consistent with results from other beta-sheet model studies and with statistical analyses of interstrand residue contacts in protein crystal structures. Interaction between the side chains of Tyr-2 and Lys-9 also stabilizes the beta-hairpin conformation. Tyr-2/Lys-9 is a "diagonal" interstrand juxtaposition because these residues are not directly across from one another in terms of the hydrogen bonding registry between the strands. This diagonal interaction arises from the right-handed twist that is commonly observed among beta-sheets. Evidence of diagonal side chain-side chain contacts has been observed in other autonomously folding beta-sheet model systems, but we are not aware of other efforts to determine whether a diagonal interaction contributes to beta-sheet stability.     

Probing enantioselectivity on chirally modified Cu(110), Cu(100), and Cu(111) surfaces

Temperature programmed desorption methods have been used to probe the enantioselectivity of achiral Cu(100), Cu(110), and Cu(111) single crystal surfaces modified by chiral organic molecules including amino acids, alcohols, alkoxides, and amino-alcohols. The following combinations of chiral probes and chiral modifiers on Cu surfaces were included in this study: propylene oxide (PO) on L-alanine modified Cu(110), PO on L-alaninol modified Cu(111), PO on 2-butanol modified Cu(111), PO on 2-butoxide modified Cu(100), PO on 2-butoxide modified Cu(111), R-3-methylcyclohexanone (R-3-MCHO) on 2-butoxide modified Cu(100), and R-3-MCHO on 2-butoxide modified Cu(111). In contrast with the fact that these and other chiral probe/modifier systems have exhibited enantioselectivity on Pd(111) and Pt(111) surfaces, none of these probe/modifier/Cu systems exhibit enantioselectivity at either low or high modifier coverages. The nature of the underlying substrate plays a significant role in the mechanism of hydrogen-bonding interactions and could be critical to observing enantioselectivity. While hydrogen-bonding interactions between modifier and probe molecule are believed to induce enantioselectivity on Pd surfaces (Gao, F.; Wang, Y.; Burkholder, L.; Tysoe, W. T. J. Am. Chem. Soc. 2007, 129, 15240-15249), such critical interactions may be missing on Cu surfaces where hydrogen-bonding interactions are believed to occur between adjacent modifier molecules, enabling them to form clusters or islands.