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J C Lacey

Publications and source records attributed to J C Lacey.

At least 19 recordsLinked to original sources
PubMed1992

Preferential hydrophobic interactions are responsible for a preference of D-amino acids in the aminoacylation of 5'-AMP with hydrophobic amino acids.

We have studied the chemistry of aminoacyl AMP to model reactions at the 3' terminus of aminoacyl tRNA for the purpose of understanding the origin of protein synthesis. The present studies relate to the D, L preference in the esterification of 5'-AMP. All N-acetyl amino acids we studied showed faster reaction of the D-isomer, with a generally decreasing preference for D-isomer as the hydrophobicity of the amino acid decreased. The beta-branched amino acids, Ile and Val, showed an extreme preference for D-isomer. Ac-Leu, the gamma-branched amino acid, showed a slightly low D/L ratio relative to its hydrophobicity. The molecular basis for these preferences for D-isomer is understandable in the light of our previous studies and seems to be due to preferential hydrophobic interaction of the D-isomer with adenine. The preference for hydrophobic D-amino acids can be decreased by addition of an organic solvent to the reaction medium. Conversely, peptidylation with Ac-PhePhe shows a preference for the LL isomer over the DD isomer.

Acylation↗
PubMed1992

Experimental studies on the origin of the genetic code and the process of protein synthesis: a review update.

This article is an update of our earlier review (Lacey and Mullins, 1983) in this journal on the origin of the genetic code and the process of protein synthesis. It is our intent to discuss only experimental evidence published since then although there is the necessity to mention the old enough to place the new in context. We do not include theoretical nor hypothetical treatments of the code or protein synthesis. Relevant data regarding the evolution of tRNAs and the recognition of tRNAs by aminoacyl-tRNA-synthetases are discussed. Our present belief is that the code arose based on a core of early assignments which were made on a physico-chemical and anticodonic basis and this was expanded with new assignments later. These late assignments do not necessarily show an amino acid-anticodon relatedness. In spite of the fact that most data suggest a code origin based on amino acid-anticodon relationships, some new data suggesting preferential binding of Arg to its codons are discussed. While information regarding coding is not increasing very rapidly, information regarding the basic chemistry of the process of protein synthesis has increased significantly, principally relating to aminoacylation of mono- and polyribonucleotides. Included in those studies are several which show stereoselective reactions of L-amino acids with nucleotides having D-sugars. Hydrophobic interactions definitely play a role in the preferences which have been observed.

5'-Nucleotidase↗
PubMed1991

Stereoselective, nonenzymatic, intramolecular transfer of amino acids.

Biological systems synthesize proteins with an almost exclusive use of L-amino acids and virtually none of the D isomer. There has been no satisfactory explanation for the origin of this use of the L isomer. Research presented here shows that at pH 5, transfer of phenylalanine from the adenylate anhydride to ester occurs and is 95-97% efficient for the L isomer and only about 50% efficient for the D isomer. The origin of the use of the L isomer, given D-ribose nucleotides, may be based in part on this stereoselectivity.

Adenosine Monophosphate↗
PubMed1991

Stereoselective formation of bis(alpha-aminoacyl) esters of 5'-AMP suggests a primitive peptide synthesizing system with a preference for L-amino acids.

In the biosynthesis of proteins, each amino acid passes from the aminoacyl adenylate to become an amino acid ester and finally a 2' (3') peptidyl ester of the AMP residue at the end of a tRNA. Consequently, the chemistry of protein synthesis is the chemistry of aminoacyl and peptidyl AMP. Our data has revealed properties of 5'-AMP and its esters which should allow the preferential catalytic synthesis of L-amino acid peptides via a bis(2', 3'-aminoacyl) ester intermediate. Results in this paper concern one step in the proposed process and show that preexisting Ac-L-Phe monoester reacts about 2.5-times faster to form diester than preexisting Ac-D-Phe monoester.

Adenosine Monophosphate↗
PubMed1990

Was there a universal tRNA before specialized tRNAs came into existence?

It is generally true that evolving systems begin simply and become more complex in the evolutionary process. For those who try to understand the origin of a biochemical system, what is required is the development of an idea as to what simpler system preceeded the present one. Here we present an hypothesis that a universal tRNA molecule, capable of reading many codons may have preceeded the appearance of individual tRNAs. Evidence seems to suggest that this molecule may have been derived from a common ancestor of the contemporary 5S rRNAs and tRNAs.

Biological Evolution↗
PubMed1990

Chemical esterification of 5'-AMP occurs predominantly at the 2' position.

We describe experiments here which show that chemical esterification of 5'-adenylic acid (5'-AMP) with N-acetyl D- or L-phenylalanine (Ac-D- or Ac-L-Phe) imidazolide occurs principally, if not exclusively, at the 2' position. Furthermore, in experiments with the formation of the 2'-3' diester with butyric acid and N-acetyl glycine (Ac-Gly), we found the second esterification was also predominantly at the 2' position. This means that mixed diesters can be predictably prepared with the positions of the substituents known. The results are consistent with a model for the preferential catalytic synthesis of L-based peptides via a 2'-3' diester intermediate of purine monoribonucleotides.

Adenosine Monophosphate↗
PubMed1990

Ribonucleic acids may be catalysts for the preferential synthesis of L-amino acid peptides: a minireview.

This minireview is a summary of the basic concepts and pieces of experimental evidence supporting a hypothesis that suggests a mechanism whereby purine monoribonucleotides having D-ribose may be able to preferentially catalyze the synthesis of L-amino acid peptides. The proposed mechanism involves a 2'-3' diaminoacyl intermediate and the preference accrues from several factors that favor the L-isomer, principally for hydrophobic amino acids. Although the hypothesis has not been fully tested, some crucial evidence has been published. Other pieces of evidence are now being submitted or are in press for publication and still other experiments, principally on the step of peptide bond formation, are in the process of being carried out. The purpose of a review at this point is to present the hypothesis to the scientific community in hopes of generating discussion, suggestions, and evaluation by other workers. Should the hypothesis prove correct, it may represent the most primitive and fundamental relationship between the nucleic acid and protein systems. In addition, it would represent another important example of the catalytic ability of RNA.

Amino Acids↗
PubMed1988

Evolution of E. coli tRNA(Trp).

Earlier studies (1) have shown there are direct correlations between the hydrophobicity ranking of most amino acids and their anticodonic nucleotides. However, four anticodonic assignments, i.e. those for Trp, Tyr, Ile and the XGA anticodons for Ser, did not correlate. It was our proposal that this failure to correlate was due to the fact that these assignments were made late, relative to the bulk of the assignments, in evolution through the mutation of existing tRNAs. We have shown (2) that E. coli tRNA(Ile 1) and tRNA(Ile 2) were likely derived from tRNA(Val 1) and tRNA(Lys) respectively and E. coli tRNA(Tyr) was possibly derived from E. coli 5s rRNA or a common precursor with 5s rRNA (3). The fact that quite high homologies were observed in these comparisons is consistent with the late evolution of the tRNAs in question. We now examine the evolution of E. coli tRNA(Trp) by comparing its homology with other E. coli tRNAs. The data suggest a possible evolutionary relationship with E. coli tRNA(Gly) or tRNA(Arg). The data support the idea of the late assignment of anticodons to Trp.

Anticodon↗
PubMed1988

Differential distribution of D and L amino acids between the 2' and 3' positions of the AMP residue at the 3' terminus of transfer ribonucleic acid.

Amino acids esterified to the ribose group of 5'-adenylic acid (AMP) constantly migrate between the 2' and 3' positions of the ribose at a rate of several times per second, which is slower than the rate of peptide-bond synthesis (15-20 per sec). Because the contemporary protein-synthesizing system only incorporates amino acids into protein when they are at the 3' position of the AMP at the terminus of tRNA, the value of the equilibrium constant relative to the 2' and 3' positions is of considerable interest. Differences between D and L isomers in this regard might be especially revealing. We have used N-acetylaminoacyl esters of AMP as models for the 3' terminus of tRNA and find that glycine and the L amino acids consistently distribute predominantly to the 3' position (approximately equal to 67% 3', approximately equal to 33% 2'), but D amino acids distribute to that position generally to a lesser extent and in a manner inversely related to the hydrophobicity of the amino acid side chain. This consistency of the L amino acid preference for the 3' position, combined with the inconsistency of the D amino acid preference, may be one reason for the origin of our contemporary protein-synthesizing system, which forms the peptide bond preferentially with L amino acids and only when they are in the 3' position of the ribose moiety of the AMP residue at the 3' terminus of every tRNA.

Adenosine Monophosphate↗
PubMed1986

Comparative rates of esterification of 5'-AMP with hydrophobic amino acids: relevance to the genetic-code assignments.

We have continued our program aimed at understanding the origin and evolution of the genetic code and the process of protein synthesis by comparing the rates of esterification of 5'-AMP by a series of hydrophobic N-acetylamino acids. The reaction clearly shows differences in reaction rate (AcPhe greater than AcLeu greater than AcVal greater than AcIle) among the amino acids having A as middle letter of their anticodons. However, there were no significant differences in reaction rate between AcLeu, AcNorleu, and Ac-alpha-aminobutyric acid, and AcGly reacted faster than all of these and AcPhe. Consequently, this simple reaction with AMP can distinguish only among those amino acids that actually have A as the middle anticodonic nucleotide. The relevance of these studies to the origins of the process of protein synthesis and of the genetic code is discussed in conjunction with results from other studies of a similar nature.

Acetylation↗
PubMed1986

Aliphatic amino acid side chains associate with the "face" of the adenine ring.

We have synthesized the free amino acid adenylate anhydrides of phenylalanine, leucine, isoleucine and valine. These activated compounds are very labile at high pH, but at low pH they become more stable. Proton NMR spectra of these adenylates show that in every case, the hydrophobic side chains, even in these small molecules at low pH and low concentration, are associated with the "face" of the adenine ring. Although aromatic rings are known to associate with adenine in this fashion, to our knowledge this is the first report of an intercalative-type interaction of aliphatic side chains with nucleic acid bases. Since adenine is the most hydrophobic base, these interactions are of a hydrophobic character, and occur in spite of the fact that the adenine ring is protonated. These results may have implications regarding recognition processes in DNA-protein and RNA-protein interactions.

Adenine↗
PubMed1985

Rationalization of some genetic anticodonic assignments.

The genetic code appears to be a logic matrix in which, generally speaking, there is a correlation between the hydrophobicities of amino acids and their anticodonic nucleotides. There are several exceptions to this generality, however, and using previous data on hydrophobicity and binding constants, coupled with new data on reaction rates, we rationalize several of the anticodonic assignments.

Amino Acids↗
PubMed1985

Chirally selective, intramolecular interaction observed in an aminoacyl adenylate anhydride.

All earthly creatures use only L-amino acids in template directed protein synthesis. The reason for this exclusive use of the L-isomer is not yet apparent, although recent experiments by Usher and his colleagues have shown some stereoselectivity in the aminoacylation of di- and polynucleotides. We have separately reported on intramolecular interactions between hydrophobic amino acid side chains and the adenine ring in aminoacyl adenylates. There was a preferential association of Phe greater than Leu = Ile greater than Val with the adenine in these studies, but we made no attempts to address the question of D, L selectivity. Recently, in 1H NMR studies of N-acetylphenylalanyl adenylate anhydride, we noticed evidence that both D- and L-isomers of the amino acid were present and, furthermore, that one isomer seemed to be associating with the adenine ring more strongly than the other. Using HPLC, we have separated the two diastereoisomers and have enzymatically determined that the isomer which associates more strongly is the biologically important one, the L-isomer. We present those studies here and discuss the evolutionary significance of this finding.

Adenosine Monophosphate↗
PubMed1978

Genetic code correlations: amino acids and their anticodon nucleotides.

The data here show direct correlations between both the hydrophobicity and the hydrophilicity of the homocodonic amino acids and their anticodon nucleotides. While the differences between properties of uracil and cytosine derivatives are small, further data show that uracil has an affinity for charged species. Although these data suggest that molecular relationships between amino acids and anticodons were responsible for the origin of the code, it is not clear what the mechanism of the origin might have been.

Amino Acids↗
PubMed1976

Interactions of hydrated metal ions with nucleotides: the crystal structure of barium adenosine 5'-monophosphate heptahydrate.

The crystal and molecular structure of barium adenosine 5'-monophosphate heptahydrate was determined from x-ray diffraction data. Crystals of barium adenosine 5'-monophosphate heptahydrate are monoclinic, space group C2, with a = 32.559(3), b = 6.969(3), c = 9.597(1) A, and beta = 100.31(1) degrees. Intensity data were collected with an automated diffractometer. The structure was solved by the heavy-atom method and refined by least-squares to R = 0.034. This structure provides an example of an outer-sphere metal-nucleotide complex, in which a completely hydrated metal ion interacts with the nucleotide only through water bridges. The barium ion is coordinated to eight water molecules, which form a slightly distorted square antiprism. Seven of the eight water molecules from the barium hydration shell are hydrogen bonded to phosphate groups; three of these water molecules are also hydrogen bonded to other suitable acceptor sites on the base and ribose moieties. The conformation about the glycosidic bond is anti, with chiCN = 69 degrees, and, as in most nucleotide structures, the conformation about the C(4')-C(5') bond is gauche-gauche. However, the ribose displays an unusual conformation (best described as C(4')-exo) not previously observed in crystal structures of nucleosides or nucleotides, other than 3',5'-cyclic nucleotides. It is possible that this unusual conformation is a consequence of the metal-water-nucleotide bridging interactions.

Adenosine Monophosphate↗