Localized unfolding of collagen explains collagenase cleavage near imino-poor sites

Collagenases cleave all three chains of type III collagen at specific sites characterized by a Gly-Leu or a Gly-Ile bond that is upstream from an imino acid-poor region. Molecular dynamics trajectories were used to calculate the free energy of unfolding for collagen-like model peptides. The free energy profiles suggest that such imino-poor regions can adopt a low-energy, partially unfolded state where one of the peptide chains forms a solvent-exposed loop. The results are consistent with a model for collagenase cleavage where partial unfolding of imino-poor regions enables collagenases to gain access to their cleavage sites.     

Complexity in orchestration of chemical groups near different cleavage sites in RNase P RNA mediated cleavage

RNase P mediated cleavage of the tRNA(His) precursor does not rely on the formation of the +73/294 interaction to give the correct cleavage product, i.e. cleavage at -1, while other tRNA precursors that are cleaved at the canonical site +1 do. A previous model, here referred to as the 2'OH-model, predicts that the 2'OH at the canonical cleavage site would affect cleavage at -1. Here we used model RNA hairpin substrates mimicking the structural architecture of the tRNA(His) precursor cleavage site to investigate the role of 2'OH with respect to ground state binding and rate of cleavage in the presence and absence of the +73/294 interaction. Our data emphasize the importance of the 2'OH in the immediate vicinity of the scissile bond. Moreover, introduction of 2'H at the cleavage site did not affect cleavage at an alternative cleavage site to any significant extent. Our findings are therefore inconsistent with the 2'OH model. We favor a model where the 2'OH at the cleavage site influence Mg2+ binding in its vicinity, however we do not exclude the possibility that the 2'OH at the cleavage site interacts with RNase P RNA. Studying the importance of the 2'OH at different cleavage sites also indicated a higher dependence on the 2'OH at the cleavage site in the absence of the +73/294 interaction than in its presence. Finally, we provide data suggesting that N3 of U at position -1 in the substrate is most likely not involved in an interaction with RNase P RNA.     

Recognition of substrates by tyrosylprotein sulfotransferase. Determination of affinity by acidic amino acids near the target sites.

The sulfation of proteins by tyrosylprotein sulfotransferase (TPST) is highly site-specific. In this study, we examined the sequence specificity of the target site for TPST by determining the kinetics of rat liver TPST with peptides related to the sequence of the C4 component of complement. The data obtained from this study demonstrate that selective elimination of negative charges from the -5 to +5 region of the acceptor tyrosine, either by removal or by isosteric substitution or the acidic amino acids in the region, produced a substantial change in the Km value, with relatively little effect on Vmax. Substitutions at -1 and +1 positions increase the Km value by 22- and 4-fold, respectively, whereas removal of the acidic amino acids from the -5, -4, or +4 positions increased the Km values by a factor of 2-4. The effect of elimination of an acidic amino acid on the Km value was constant and specific for its particular position in relation to tyrosine, and the effect of modification of more than one amino acid was multiplicative. This study provides evidence that: 1) acidic residues near tyrosines promote sulfation by increasing the affinity of enzyme-substrate binding and have little effect on catalytic rate; 2) the contribution of each acidic residue to affinity for TPST is independent and varies according to position relative to the acceptor tyrosine; and 3) the enzyme interacts with a segment of at least 4-5 residues on each side of the tyrosine, with the residues on the -1 and +1 positions being the most important determinants. In general, residues on the NH2-terminal side of the tyrosine have a greater effect on affinity for TPST.     

Evaluation of superior BACE1 cleavage sequences containing unnatural amino acids

A recombinant form of BACE1 (β-site amyloid precursor protein cleaving enzyme-1) corresponding to positions 46-454 of the extracellular domain of the original membrane enzyme was prepared. The recombinant BACE1 (rBACE1) had the kinetic parameters K(m)=5.5μM and k(cat)=1719s(-1). Using several libraries of substrates containing unnatural amino acids, the specificity of rBACE1 was evaluated. LC/MS of digests derived from the libraries clarified that a dodecapeptide containing unnatural amino acids at P(2) to [Formula: see text] was a superior cleavage sequence.     

Free amino acids in the early cleavage stages of the rabbit egg

In the first half of gestation, mouse yolk sac contains levels of N-acetyl-β-hexosaminidase activity and a ratio of N-acetyl-β-hexosaminidase: β-glucuronidase much higher than those of other embryonic tissues or the decidua. The properties of the yolk sac enzyme are very similar to those in the other tissues, suggesting that the observed difference in activity is quantitative rather than qualitative. In blastocyst cultures, the vesicular growths derived from the inner cell mass possess patterns of N-acetyl-β-hexosaminidase activity similar to yolk sac in vivo, but different from trophoblast cells developing in the same cultures. It is therefore proposed that the vesicular growths contain at least some differentiated yolk sac cells.     

Differences in hydration structure near hydrophobic and hydrophilic amino acids.

We use molecular dynamics to simulate recent neutron scattering experiments on aqueous solutions of N-acetyl-leucine-amide and N-acetyl-glutamine-amide, and break down the total scattering function into contributions from solute-solute, solute-water, water-water, and intramolecular correlations. We show that the shift of the main diffraction peak to smaller angle that is observed for leucine, but not for glutamine, is attributable primarily to alterations in water-water correlations relative to bulk. The perturbation of the water hydrogen-bonded network extends roughly two solvation layers from the hydrophobic side chain surface, and is characterized by a distribution of hydrogen bonded ring sizes that are more planar and are dominated by pentagons in particular than those near the hydrophilic side chain. The different structural organization of water near the hydrophobic solute that gives rise to the inward shift in the main neutron diffraction peak under ambient conditions may also provide insight into the same directional shift for pure liquid water as it is cooled and supercooled.     

Patterns of intramolecular carbon isotopic heterogeneity within amino acids of autotrophs and heterotrophs

A survey of the intramolecular C isotopic composition of a variety of organisms was conducted to investigate the potential of intramolecular isotopic measurements as a tracer of biological or geochemical processes. Based on a consideration of inorganic C sources and enzymatic fractionations, contrasting predictions were made for the relative ¹³C enrichments of the -carboxyl carbons fixed by the anapleurotic ()-carboxylation pathway during amino acid synthesis by photoautotrophs and heterotrophs. To test the model predictions, the stable C isotopic compositions of the acid hydrolyzable C fraction, the total amino acid -carboxyl C fraction and the -carboxyl C of glutamate from a variety of autotrophic and heterotrophic organisms were compared. The relative ¹³C enrichments of carboxyl carbons in the bulk amino acid fraction and in glutamate conformed qualitatively to model predictions. Macroalgal taxa possessed a significantly less enriched carboxyl C fraction than did either C3 or C4 vascular plants, indicating the presence of a different -carboxylation pathway operating in these organisms. In most multicellular heterotrophs, the isotopic composition of the amino acid carboxyl carbons closely resembled that of their food sources. Amino acids are apparently assimilated into tissue proteins directly from their diets without significant metabolic modification. However, shifts in the isotopic composition of the carboxyl C fractions in some organisms were detected that were consistent with the occurrence of significant resynthesis of amino acids from non-amino acid precursors. Comparison of plant leaves and roots provided evidence of environmentally controlled assimilate partitioning. Intramolecular isotopic measurements of biological molecules provide unique insights into the origins and transformations of bio-molecules.     

Enantioselective binding sites on bovine serum albumin to dansyl amino acids.

The enantioselective binding sites on bovine serum albumin were examined by HPLC using 19 racemic 5-N, N-dimethylamino-1-naphthalenesulfonyl derivatives of alpha-amino acids (dansyl amino acids) as chiral probes. On a bovine serum albumin bonded chiral stationary phase, seven L-forms eluted faster than their D-forms, while ten D-forms eluted before their L-forms. It was speculated that either two classes or two different binding sites exist on bovine serum albumin which can be distinguished by N-dansyl-L-proline and N-dansyl-D-norvaline. This was confirmed by fluorometric experiments where non-fluorescent 1-naphthalenesulfonyl derivatives were synthesized and competitive adsorption experiments were performed.     

Distribution of amino acids in functional sites of proteins with high melting temperature

The stability of proteins in its native state has an important implication on its function and evolution. The functional site analysis may lead to better understanding of how these amino acid distributions influence the melting temperature of proteins. It has been reported that increasing the fraction of hydrophobic contacts in a protein tends to raise melting temperature; increasing the fraction of repulsive charge contacts decrease the melting temperature and consistent with a destabilizing effect. The role of amino acid distribution as hydrophobic, charged and polar residues in proteins and mainly in its functional sites has been studied. Due to limited data availability, redundancy check and controlled environment parameters, the study was carried out with ten single chain-wild proteins having melting temperature above 80°C at pH 7. The analysis depicts that, the entire protein, hydrophobic residues are more frequent in single chain proteins and charged residues are more frequent in multi-chains proteins. In functional sites of these proteins, hydrophobic and charged residues are equally frequent in single chain proteins and charged residues are very high in multi-chains proteins. But, the polar residue distribution remains same for both single chain and multi-chain proteins and its functional sites.     

Sense codon-dependent introduction of unnatural amino acids into multiple sites of a protein

Cell-free protein synthesis, driven by a crude S30 extract from Escherichia coli, has been applied to the preparation of proteins containing unnatural amino acids at specific positions. We have developed methods for inactivating tRNA(Asp) and tRNA(Phe) within a crude E. coli tRNA by an antisense treatment and for digesting most of the tRNA within the S30 extract without essential damage to the ribosomal activity. In the present study, we applied these methods to the substitution of Asp and Phe residues of the HIV-1 protease with unnatural amino acids. With 10 mM Mg(2+), the translation efficiency was higher than that with the other tested concentration, and the misreading efficiency was low. The protease mRNA was translated in the presence of an antisense DNA-treated tRNA mixture and 2-naphthylalanyl- and/or p-phenylazophenylalanyl-tRNA. The results suggest that a good portion of the translation products are substituted at all of the seven positions originally occupied by Asp or Phe.     

Widespread occurrence of specific, high affinity binding sites for amino acids.

The high affinity binding of several amino acids to various membrane and protein preparations has been measured. Binding of radioactive amino acids suspected of being neurotransmitters and also of leucine and tyrosine to brain, liver and heart muscle membranes was saturable, reversible and stereospecific. Similar characteristics were found using chloroform-methanol extracted brain tissue and heat denatured albumin. Compounds thought to act as blockers of postsynaptic binding such as strychnine, bicuculline and kainic acid did not inhibit binding. Thus, specific high affinity interactions between amino acids and proteins are widespread and largely unrelated to neurotransmission.     

RF1 knockout allows ribosomal incorporation of unnatural amino acids at multiple sites

Stop codons have been exploited for genetic incorporation of unnatural amino acids (Uaas) in live cells, but their low incorporation efficiency, which is possibly due to competition from release factors, limits the power and scope of this technology. Here we show that the reportedly essential release factor 1 (RF1) can be knocked out from Escherichia coli by 'fixing' release factor 2 (RF2). The resultant strain JX33 is stable and independent, and it allows UAG to be reassigned from a stop signal to an amino acid when a UAG-decoding tRNA-synthetase pair is introduced. Uaas were efficiently incorporated at multiple UAG sites in the same gene without translational termination in JX33. We also found that amino acid incorporation at endogenous UAG codons is dependent on RF1 and mRNA context, which explains why E. coli tolerates apparent global suppression of UAG. JX33 affords a unique autonomous host for synthesizing and evolving new protein functions by enabling Uaa incorporation at multiple sites.     

Caspase-dependent cleavage of nucleic acids

Autoimmune diseases are frequently characterized by the presence of autoantibodies directed against nucleic acid-protein complexes present in the nucleus of the cell. The mechanisms by which these autoantigenic molecules escape immunological tolerance are largely unknown, although a number of recent observations suggest that modified self-proteins generated during apoptosis may play an important role in the development of autoimmunity. It has been hypothesized that the recognition of these modified self-proteins by the immune system may promote autoantibody production. While apoptosis is specifically characterized by posttranslational modification of proteins, recent findings also show that nucleic acids are modified. This review summarizes the specific cleavages of some of these key nucleic acids, i.e. chromosomal DNA, ribosomal RNA and small structural RNAs (U1 snRNA, Y RNA), in apoptotic cells.     

Receptor sites for amino acids in the facial taste system of the channel catfish

1. Receptor sites for different amino acids in the facial taste system of the channel catfish, Ictalurus punctatus, were determined from in vivo electrophysiological cross-adaptation experiments. 2. Relatively independent receptor sites were indicated for L-proline, D-proline, D-arginine, L-histidine and L-lysine, as well as those previously reported for L-alanine, L-arginine and D-alanine. 3. The functional isolation of two nerve twigs that were more responsive to D-alanine than to L-alanine or to other test stimuli provided further evidence for the existence of D-alanine sites that are independent from those to L-alanine. 4. Under all cross-adaptation regimes, the taste responses to the majority of test stimuli were reduced. Various possible mechanisms accounting for this generalized reduction in action potential activity during adaptation are discussed.     

Effects of the metabolites of the branched-chain amino acids and cysteamine on the glycine cleavage system

The effects of ten metabolites of the branched-chain amino acids, CoA and cysteamine (beta-mercaptoethylamine), on the glycine cleavage system were investigated with the liver extracts. It was found that CoA derivatives including tiglyl CoA, isobutyryl CoA, succinyl CoA, methylmalonyl CoA, isovaleryl CoA, propionyl CoA and CoA itself and cysteamine significantly inhibited the glycine cleavage system of the liver extracts. Further studies on the glycine-14CO2 exchange catalyzed by p-protein and H-protein purified from chicken liver indicated that tiglyl CoA inhibited the activity of P-protein in an apparently competitive manner with respect to H-protein, and that cysteamine inhibited the activity of P-protein in two ways, by increasing the Km value for glycine and changing Vmax.     

High-yield cell-free protein synthesis for site-specific incorporation of unnatural amino acids at two sites

Using aminoacyl-tRNA synthetase/suppressor tRNA pairs derived from Methanocaldococcus jannaschii, an Escherichia coli cell-free protein production system affords proteins with site-specifically incorporated unnatural amino acids (UAAs) in high yields through the use of optimized amber suppressor tRNA(CUA)(opt) and optimization of reagent concentrations. The efficiency of the cell-free system allows the incorporation of trifluoromethyl-phenylalanine using a polyspecific synthetase evolved previously for p-cyano-phenylalanine, and the incorporation of UAAs at two different sites of the same protein without any re-engineering of the E. coli cells used to make the cell-free extract.     

Transformation of some hydroxy amino acids to other amino acids.

It has been observed that beta-hydroxy-alpha-amino acids are transformed into other amino acids, when heated in dilute solutions with phosphorous acid, phosphoric acid or their ammonium salts. It has been shown that as in the case of previously reported glycine-aldehyde reactions, glycine also reacts with acetone to give beta-hydroxyvaline under prebiologically feasible conditions. It is suggested, therefore, that the formation of beta-hydroxy-alpha-amino acids and their transformation to other amino acids may have been a pathway for the synthesis of amino acids under primitive earth conditions.