Catalytic peptide assemblies.

Self-assembly of molecules often results in new emerging properties. Even very short peptides can self-assemble into structures with a variety of physical and structural characteristics. Remarkably, many peptide assemblies show high catalytic activity in model reactions reaching efficiencies comparable to those found in natural enzymes by weight. In this review, we discuss different strategies used to rationally develop self-assembled peptide catalysts with natural and unnatural backbones as well as with metal-containing cofactors.

Construction and analysis of base-paired regions of the 16S rRNA in the 30S ribosomal subunit determined by constraint satisfaction molecular modelling.

Structure models for each of the secondary structure regions from the Escherichia coli 16S rRNA (58 separate elements) were constructed using a constraint satisfaction modelling program to determine which helices deviated from classic A-form geometry. Constraints for each rRNA element included the comparative secondary structure, H-bonding conformations predicted from patterns of base-pair covariation, tertiary interactions predicted from covariation analysis, chemical probing data, rRNA-rRNA crosslinking information, and coordinates from solved structures. Models for each element were built using the MC-SYM modelling algorithm and subsequently were subjected to energy minimization to correct unfavorable geometry. Approximately two-thirds of the structures that result from the input data are very similar to A-form geometry. In the remaining instances, the presence of internal loops and bulges, some sequences (and sequence covariants) and accessory information require deviation from A-form geometry. The structures of regions containing more complex base-pairing arrangements including the central pseudoknot, the 530 region, and the pseudoknot involving base-pairing between G570-U571/A865-C866 and G861-C862/G867-C868 were predicted by this approach. These molecular models provide insight into the connection between patterns of H-bonding, the presence of unpaired nucleotides, and the overall geometry of each element.

Initiation factor 3-induced structural changes in the 30 S ribosomal subunit and in complexes containing tRNA(f)(Met) and mRNA.

Initiation factor 3 (IF3) acts to switch the decoding preference of the small ribosomal subunit from elongator to initiator tRNA. The effects of IF3 on the 30 S ribosomal subunit and on the 30 S.mRNA. tRNA(f)(Met) complex were determined by UV-induced RNA crosslinking. Three intramolecular crosslinks in the 16 S rRNA (of the 14 that were monitored by gel electrophoresis) are affected by IF3. These are the crosslinks between C1402 and C1501 within the decoding region, between C967xC1400 joining the end loop of a helix of 16 S rRNA domain III and the decoding region, and between U793 and G1517 joining the 790 end loop of 16 S rRNA domain II and the end loop of the terminal helix. These changes occur even in the 30 S.IF3 complex, indicating they are not mediated through tRNA(f)(Met) or mRNA. UV-induced crosslinks occur between 16 S rRNA position C1400 and tRNA(f)(Met) position U34, in tRNA(f)(Met) the nucleotide adjacent to the 5' anticodon nucleotide, and between 16 S rRNA position C1397 and the mRNA at positions +9 and +10 (where A of the initiator AUG codon is +1). The presence of IF3 reduces both of these crosslinks by twofold and fourfold, respectively. The binding site for IF3 involves the 790 region, some other parts of the 16 S rRNA domain II and the terminal stem/loop region. These are located in the front bottom part of the platform structure in the 30 S subunit, a short distance from the decoding region. The changes that occur in the decoding region, even in the absence of mRNA and tRNA, may be induced by IF3 from a short distance or could be caused by the second IF3 structural domain.

Effects of tetracycline and spectinomycin on the tertiary structure of ribosomal RNA in the Escherichia coli 30 S ribosomal subunit.

Structural analysis of the 16 S rRNA in the 30 S subunit and 70 S ribosome in the presence of ribosome-specific antibiotics was performed to determine whether they produced rRNA structural changes that might provide further insight to their action. An UV cross-linking procedure that determines the pattern and frequency of intramolecular 16 S RNA cross-links was used to detect differences reflecting structural changes. Tetracycline and spectinomycin have specific effects detected by this assay. The presence of tetracycline inhibits the cross-link C967xC1400 completely, increases the frequency of cross-link C1402x1501 twofold, and decreases the cross-link G894xU244 by one-half without affecting other cross-links. Spectinomycin reduces the frequency of the cross-link C934xU1345 by 60% without affecting cross-linking at other sites. The structural changes occur at concentrations at which the antibiotics exert their inhibitory effects. For spectinomycin, the apparent binding site and the affected cross-linking site are distant in the secondary structure but are close in tertiary structure in several recent models, indicating a localized effect. For tetracycline, the apparent binding sites are significantly separated in both the secondary and the three-dimensional structures, suggesting a more regional effect.

Measurement and interpretation of Q0 and Q1 band property changes of two cationic metalloporphyrins upon binding with B-DNA: electronic MCD, CD, and optical absorption.

Room-temperature Q-band electronic MCD, CD, and optical spectra are reported for the first time for two free and nucleic acid-bound cationic metalloporphyrins. Metalloporphyrins are the high-symmetry (C4v or D4h), four-coordinate tetragonal type MP(X) [M = CuII and PtII; P(X) = meso-tetrakis(X-N-methylpyridyl)porphine; X = 2 or 4], and the nucleic acid is native, B-form calf thymus DNA (CT DNA). For intercalation system PtP(4)/CT DNA, large optical (lambda 0, epsilon max) and MCD (lambda peak, lambda trough, A(aj), A(aj)/D(aj), and delta[theta]Mp-t/epsilon max) band parameter shifts, as well as a single negative (-) induced CD peak for each of Q0 and Q1, were observed upon binding of the porphyrin to chiral DNA. The directions and magnitudes of these changes are comparable to those observed for the Soret (B0) band of this system. Decreases of MCD/optical ratio delta[theta]Mp-t/epsilon max (varies; is directly proportional to A(aj)/D(aj)) of 30% (Q0) and 50% (Q1) upon intercalation indicate substantial reductions of the Q0[1Eu(a) (0,0), approximately 1a1u1 4eg1] and Q1[1Eu(a)(0,1), approximately 1a1u1 4eg1] excited state angular momenta, . It is of additional interest that intercalation leads to intensity cancellation of one of the four A-term lobes, the (+)lobe of the Q0 MCD (+)pseudo-A-term, which was also observed previously for intercalation systems PdP(4)/poly(G-C)2 and /CT DNA. Application of the CD sector method to the constituent x- and y-polarized porphyrin edtms, square root of D(aj), of the Q0 (edtms mu0x and mu0y) and Q1 (edtms mu1x and mu1y) CD bands leads to the conclusion that PtP(4) is symmetrically intercalated between adjacent GC base pairs, specifically at 5'GC3' sites, with each of two adjacent 4-N-methylpyridyl groups extending into each of the major and minor grooves. For outside binder CuP(2), small optical and MCD band parameter shifts and smaller, single positive (+) induced CD peaks are observed for Q0 and Q1 upon interaction with CT DNA, similar to what is found for B0. Little or no change in the MCD/optical ratio, delta[theta]Mp-t/epsilon max, informs that external binding has only small effects on the excited state angular momenta, , of these bands. The composite of MCD, CD, and optical spectra are consistent with CuP(2) binding to CT DNA by one or both of two competing external modes, i.e., by an AT-specific, edge-on minor groove mode at 5'TA3' sites and/or a face-on major groove mode with high selectivity for 5'AT3' or 5'CG3' sites. For Q0 and Q1 of each of the CuP(2)/CT DNA and PtP(4)/CT DNA systems, we observe that the genuine MCD (+) A-terms of these free MP(X)s retain their (+) sign on becoming pseudo-A-terms upon binding to the low-symmetry, asymmetric DNA sites, and this indicates that the external and intercalative modes result in the 4eg splitting, or delta LUMO, being less than the magnitude of 1a1u-3a2u energy separation, or delta HOMO.

Three-wheel and four-wheel all-terrain vehicle injuries in children.

In January 1988, sales of new three-wheel all-terrain vehicles (ATVs) were banned in the United States because of the high incidence of injury associated with their use, especially by children. Four-wheel ATVs remain on the market. A retrospective review of all ATV injuries seen in a level I pediatric trauma center was conducted to compare the nature and severity of injuries in three-wheel vehicles with those associated with four-wheelers. A total of 36 ATV injuries were seen from April 1986 to August 1988. All patients were less than 16 years of age; 72% were less than or equal to 12 years of age. Of the patients, 56% were boys; 44% were girls. Although 56% of incidents involved three-wheelers, a larger number of more serious injuries, defined as the presence of indicators of injury severity (eg, death, Injury Severity Score greater than or equal to 10, intensive care unit admission, or need for surgery), involved four-wheel vehicles. A total of 15 injuries occurred in 1987; 12 injuries, including the first death involving an ATV at the pediatric trauma center, occurred in the 7 months since the sales ban. Immature judgment and/or motor skills were the most common factors contributing to injury. Existing information regarding injuries involving three-wheel ATVs is supported by our data, according to which it is suggested that four-wheel vehicles may be dangerous in the hands of immature or unskilled operators less than 16 years of age. Injury prevention efforts should be directed at prohibiting any ATV use by persons less than 16 years of age.