On the tertiary structure of transfer ribonucleic acid

Melcher, Gerhard

doi:10.1016/0014-5793(69)80130-4

Cited by 24 publications

(5 citation statements)

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“…Models like a symmetrical H-model [2] or almost symmetrical arrangements by folding all arms together [34] can be excluded, whereas others are compatible with the results [4,32,35].…”

Section: Discussionsupporting

confidence: 71%

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On the Conformation of Phenylalanine Specific Transfer RNA Studies on Size and Shape of the Molecule by X‐Ray Small Angle Scattering

Pilz

Kratky

Cramer

et al. 1970

European Journal of Biochemistry

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The scattered X-ray intensities from dilute solutions of tRNAPhe (yeast) in 0.05 M Tris buffer at pH 7.5 were measured at 17". The radius of gyration R (24.4 A), the molecular weight M (26100) and the volume V (41500 A3) were determined.A comparison of experimental with theoretical scattering curves of different bodies shows that the shape of the molecule cannot be well represented by a simple triaxial body. The calculated scattering curves which fit the measured scattering data best are for an elongated body with two different cross-sections.No significant change of X-ray small angle scattering was observed on increasing the temperature from 17" to 40". At higher temperatures the radius of gyration is increased with increasing temperature and at 70' the molecule has a random coil conformation.To get more detailed information about the process of activation of amino acids during protein synthesis by the tRNA-aminoacyl synthetase system a detailed knowledge of the structure of tRNA is necessary. Although several sequences (= primary structures) of tRNAs are known, one cannot derive secondary and tertiary structures from these sequences. I n this respect the situation is similar to that in the protein field.The method of X-ray small angle scattering yields information on shape and dimensions of macromolecules in solution [I]. Previously a mixture of tRNAs [2] as well as purified tRNAaa (yeast) [3] and tRNAVa11 ( E . COG) [4] were investigated by this method. I n these investigations the temperature dependence of the scattering was not studied. We carried out our measurements with a pure species of tRNAPhe (yeast) over a wide temperature range. Our preliminary results were communicated briefly elsewhere [5]. EXPERIMENTAL PROCEDUREMaterials tRNAPhe (baker's yeast) was purified 42-fold from bulk tRNA from yeast (Boehringer Mannheim GmbH, Mannheim) by combination of extraction [6] and benzoyl-DEAE-cellulose chromatography [7]. It was chargeable to 82°/0 when tested as described [S] and no foreign activity was found in the test by MethodsThe X-ray small angle scattering measurements were carried out with Cu-K radiation. The small angle camera was a model developed in the Graz institute which is practically free from parasitic scattering [lo] ; a mechanically programmed step scanning device [Ill allowed automatic operation. The solutions were investigated in Mark-capillaries of 0.1 cm diameter. The scattered Cu-K radiation was registered with a proportional counter and pulse height discriminator ; the elimination of the KB-line was carried out by a numerical method [I21 developed in the Graz institute. A slit-shaped primary beam was used; the experimental curve therefore includes a collimation effect. This is indicated in the figures by a tilde (e. g. f, R ) . The collimation effect was elimi-

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“…Models like a symmetrical H-model [2] or almost symmetrical arrangements by folding all arms together [34] can be excluded, whereas others are compatible with the results [4,32,35].…”

Section: Discussionsupporting

confidence: 71%

“…The fact that two different cross sections are observed, rules out a simple triaxial body for the molecule. Models like a symmetrical H-model [2] or almost symmetrical arrangements by folding all arms together [34] can be excluded, whereas others are compatible with the results [4,32,35].…”

Section: Discussionmentioning

confidence: 63%

On the Conformation of Phenylalanine Specific Transfer RNA Studies on Size and Shape of the Molecule by X‐Ray Small Angle Scattering

Pilz

Kratky

Cramer

et al. 1970

European Journal of Biochemistry

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“…In this model the uniqueness of U s finds its structural expression, U s being directed into the loop-stack and being able to give a special binding possibility to the terminal adenosine residue [60]. As will be demonstrated later, it is necessary for the process of aminoacylation in this model that the terminal adenosine can only be bound to 0 ~ and N s of U s. The keto group of U s in position 4 is often replaced by sulfur, thus rendering a wrong binding more difficult.…”

Section: Double-stranded Region R Imentioning

confidence: 99%

“…The nucleotides 7 to 9 are situated on the double-stranded region R I and run through the molecular body between R I and R II [60]. The structure of these nueleotides can be compared with a knot and is of special interest due to the existence of modified bases and the ubiquitous U s .…”

Section: Double-stranded Region R Imentioning

confidence: 99%

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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“…Furthermore, except for one case [4] no conformational differences were proposed for the initiator tRNA and for the aminoacylated tRNA, and the observation that some tRNAs have several conformations dependent on cation concentration was not taken into account. The model of tRNA which we describe here exhibits at least two stable structures compatible with experimental evidence showing that aminoacyl tRNA differs from uncharged tRNA.…”

Section: A Dynamic Molecular Model For Transfer Rnamentioning

confidence: 99%

A dynamic molecular model for transfer RNA

Danchin

1971

FEBS Letters

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On the tertiary structure of transfer ribonucleic acid

Cited by 24 publications

References 5 publications

On the Conformation of Phenylalanine Specific Transfer RNA Studies on Size and Shape of the Molecule by X‐Ray Small Angle Scattering

On the Conformation of Phenylalanine Specific Transfer RNA Studies on Size and Shape of the Molecule by X‐Ray Small Angle Scattering

Tertiary structure and function of transfer-RNA

A dynamic molecular model for transfer RNA

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