Selective recognition of the native conformation of transfer ribonucleic acids by enzymes.

Lindahl, Tomas; Adams, Alice; Geroch, Mary E.; Fresco, Jacques R.

doi:10.1073/pnas.57.1.178

Cited by 49 publications

(10 citation statements)

References 11 publications

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“…According to the mechanism described above it is not necessary that the anticodon bases are recognition sites for the corresponding synthetase. The specific recognition process between t-RNA and the synthetase which would have got --during the process of evolution --an additional, more exact and dominating control mechanism, requires only that the recognition site or the recognition sites of this enzyme are on the surface of the native tertiary structure of the t-I~NA [52]. These sites may be different for every species oft-RNA.…”

Section: Process Of Aminoacylation Of T-rnamentioning

confidence: 96%

Tertiary structure and function of transfer-RNA

Melcher

1972

Biophysik

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Summary. In analogy to the globular protein structures the predominant stabilization factor of which is surface energy a compact model with the smallest possible surface of the tertiary structure of t-RNA is suggested. The principle of folding is --according to the clover leaf model --the superposition of the three leaves. The three loops form a ring (loop-stack). The stem can be placed on this molecular body bringing the CCA end into the vicinity of the loop-stack, where the CCA end can be bound. The structures of the RNA chain are subordinated to this globular structural principle. Under the influence of the GT~CG sequence the CCA end is able to undergo structural changes, thus allowing to explain the role of t-RNA in the aminoacylation process and the structural differences between t-RNA, aminoacyl-t-RNA, and peptidyl-t-RNA. Furthermore it is possible to comment on the existence of the characteristic and modified bases, the role of magnesium ions and the chemical reactions of these compounds. IntroduetionWater is necessary for the stabilization of tertiary structures of biological macromolecules. The properties of water are decisive for the arrangement of hydrophobic groups in the interior and of hydrophilic groups on the surface of the molecule. The tendency to reduce the surface as much as possible exists because free energy, the thermodynamic criterion for reaction equilibrium of the stabihty of a tertiary structure, depends on the size of the surface and the interfacial tension [84].That is the reason for the formation of micelles and why most proteins prefer globular structures in aqueous solutions. Decisive for the stability of the tertiary structure of such chain molecules like proteins and nucleic acids is the sequence, because it determines the order of the hydrophobic and hydrophilie forces and the possibilities of hydrogen bond formation. Hydrophilic groups which can be bound together in the interior of the structure by hydrogen bridges will not participate in the formation of the surface, because these bonds are energetically more favoured than hydrogen bridges of these groups with the surrounding water. Additional binding through coordinative or ionic bonds with the help of cations can be of great influence on the resulting structure.In the case of nucleic acids two groups have to be distinguished, DNA and RNA. These two classes do not only seem to differ in their stabilization principle [6i] but show also other evident differences.Generally DNA is built by two very long complementary chains. For such long complementary chains the double helix seems to be the best suited structure.

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Section: Process Of Aminoacylation Of T-rnamentioning

confidence: 96%

Tertiary structure and function of transfer-RNA

Melcher

1972

Biophysik

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“…An attempt to reveal complex formation between inactive tRNA conformers and aminoacyl-tRNA synthetase has only been made by Lindahl et al [27] for tRNALeU and leucyltRNA synthetase from yeast. Since periodate-oxidized inactive tRNA conformers were found to be able to inhibit tRNA aminoacylation some association was assumed.…”

Section: Discussionmentioning

confidence: 99%

The interaction between biologically inactive tRNA conformers and leucyl-tRNA synthetase from rabbit liver

El'skaya

Negrutskii

1987

Eur J Biochem

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The interaction between tRNA conformers inactive in aminoacylation and leucyl-tRNA synthetase has been investigated. Heat inactivation of the enzyme in the presence of inactive tRNA conformers is shown to lead to a marked increase of inactivation rate while active tRNA conformers, on the other hand, reveal a protecting effect. To study the properties of the enzyme complexed with different tRNA conformers limited proteolysis has been used. Active tRNA conformers are found to protect leucyl-tRNA synthetase against hydrolysis while inactive ones tend to intensify it. Inactive tRNA conformers are also shown to inhibit the aminoacylation of native tRNA in vitro.On the basis of these data biologically inactive conformers of animal tRNA are assumed to form an unproductive complex with leucyl-tRNA synthetase and the structure of the enzyme involved in such interaction is supposed to be more labile and 'extended' than that in complex with active tRNA conformers.Some bacterial and yeast tRNA were found to exist in vitro in forms inactive in aminoacylation and/or in interaction with ribosomes [l -31. Renaturation of the inactive form was observed after heating such tRNA in the presence of magnesium ions. Similar tRNA conformers were shown to exist in animal tissues in vivo in some extreme states of the organism such as long-term starvation [4]. The authors presented strong evidence to the effect that appearance of inactive tRNA was not due to isolation procedure such as phenol treatment. Animal inactive tRNA can be renatured in vitro by heating in conditions proposed for renaturation of inactive tRNA conformers from bacteria and yeast. Strong pH dependence was observed for renaturation in vitro and the optimal pH values were in the range of 8.0-9.0. The thermodynamic parameters for renaturation of inactive tRNA conformers isolated from rabbit liver in different extreme states of the organism are similar and the activation enthalphy value is estimated to be 120 kJ/mol, indicating a possible alteration of tRNA tertiary structure [5].The question is whether animal tRNA inactive conformers interact with components of the translation machine. The lack of tRNA acceptor capacity can be explained in two ways: either aminoacyl-tRNA synthetase cannot recognize inactive tRNA conformers or the complex formed differs somehow from the productive one. In the present paper we try to elucidate the possibility and peculiarities of the interaction between biologically inactive conformers of rabbit liver tRNA and homologous leucyl-tRNA synthetase.Correspondence to A. El'skaya, Institut Molekularnoj Biologii i Genetiki, Akademiya Nauk USSR, Zabolotnogo ulitsa, 24, Kiev, Abbreviations. tRNA"", mixture of tRNA conformers active and inactive in aminoacylation; tRNA", active tRNA conformers, rRNASepharose, rRNA immobilized on Sepharose 4B; SDS, sodium dodecyl sulfate; BD-cellulose, benzoylated DEAE-cellulose.Enzymes. Aminoacyl-tRNA synthetases (EC 6.1.1 .-); leucyltRNA synthetase (EC 6.1.1.4); trypsin (EC 3.4.21.4). USSR-252627 EXPERIMENTAL PROCED...

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“…The first one tRNA*'g with the lowest solubility in the organic phase, c& de trapped in a metastable denatured state and has been purified to an extent of 40% by Lindahl et al [3]. The third one, tRNA2, has the highest solubility in the organic phase.…”

Section: Introductionmentioning

confidence: 99%