The structure of ribonuclease in solution does not differ from its crystalline structure

Timchenko, A. A.; Ptitsyn, Oleg B.; Долгих, Д. А.; Fedorov, B.A.

doi:10.1016/0014-5793(78)80618-8

Cited by 19 publications

(11 citation statements)

References 9 publications

(2 reference statements)

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“…Since the SAXS pattern is sensitive mainly to the overall dimensions and shape of a protein molecule [17] the most probable modifications of the protein crystal structure are the changes of positions of the large structural blocks, such as protein domains and subunits [20–22]. The application of such an approach to equine liver alcohol dehydrogenase [22] and ribonuclease A [23] did not show a noticeable difference between the experimental and calculated for the crystal structure SAXS patterns. These results confirm the validity of the procedure based on the detailed description of the protein surface and demonstrate the low sensitivity of the SAXS pattern to block (domain) sliding in contrast to the locking–unlocking movements.…”

Section: Resultsmentioning

confidence: 99%

GroES co‐chaperonin small‐angle X‐ray scattering study shows ring orifice increase in solution

et al. 2000

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GroES consists of seven identical 10 kDa subunits and is involved in assisting protein folding as the partner of another oligomeric protein, the GroEL chaperonin. Here we studied the GroES structure in solution using small-angle X-ray scattering (SAXS). The SAXS pattern, calculated for the GroES crystal structure, was found to be different from the experimental one measured in solution. The synchronic shift in the radial direction and some turning of the protein subunits eliminate the difference and result in the increase of the hole diameter in the GroES ring-like structure from 8 A î in the crystal to 21 A î in solution.z 2000 Federation of European Biochemical Societies.

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Section: Resultsmentioning

confidence: 99%

GroES co‐chaperonin small‐angle X‐ray scattering study shows ring orifice increase in solution

et al. 2000

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“…Schreier and Baldwin (8) suggested that the special properties of RNase S make this protein a very suitable object for such studies. Their method involved labeling the S peptide (containing the first 20 residues from the amino terminus) with tritium and subsequently reforming an active enzyme by rapid mixing with the, remaining part of the molecule, which -consists of residues 21-124 (9). This technique yielded only the average rate of hydrogen exchange for the S peptide but still allowed the establishment ofa number of highly protected protons and showed that their individual exchange rates must be very similar.…”

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confidence: 99%

Hydrogen exchange in RNase A: neutron diffraction study.

Wlodawer¹,

Sjölin²

1982

Proc. Natl. Acad. Sci. U.S.A.

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Hydrogen exchange has been studied in a single crystal of RNase A [ribonuclease (pancreatic), EC 3.1.27.5] in the course of a neutron structure investigation. Refinement of the occupancies of amide hydrogens provided information about the kind of isotope present in each site and also provided estimates of the errors associated with the measurement. Twenty-eight-of the 120 peptide amide hydrogens were found to be at least partially protected from exchange during approximately 1 year required for crystal preparation and data collection. Most of the protected hydrogens were involved in hydrogen bonds with main-chain carbonyl groups. A contiguous region of the fl-sheet containing residues 75, 106-109, 116, and 118 had a large number of protected hydrogens, indicating its low flexibility and the lack ofaccessibility to solvent. Residues 11-13 from, the a-helix near the amino, terminus were protected, in, good agreement with a model of cooperative unwinding ofthis helix, starting from the free (amino) end.The structure of a protein revealed by the techniques of x-ray or neutron diffraction is averaged over the time period of the data collection. However, some information about the dynamic states of the molecules is also accessible. An analysis of temperature factors may provide information about short-range vibrational and librational motions (1-3), and studies ofthe amide hydrogen exchange can provide information about long-range flexibility, in the different regions of the molecule. The latter technique is based on the observation that the exchange of either deuterium or tritium for amide hydrogens can pinpoint those areas that are both accessible to solvent and sufficiently flexible for the process to take place (4).Several methods of measuring the kinetics of hydrogen exchange in order to determine the conformational equilibria of single residues (5) have been reported. When, individual amide protons are well resolved in NMR spectra, as they are in the bovine pancreatic trypsin inhibitor (6, 7), their exchange kinetics can be determined. Another possibility is to monitor the degree of exchange by following the radioactive decay of the tritium label. Schreier and Baldwin (8) suggested that the special properties of RNase S make this protein a very suitable object for such studies. Their method involved labeling the S peptide (containing the first 20 residues from the amino terminus) with tritium and subsequently reforming an active enzyme by rapid mixing with the, remaining part of the molecule, which -consists of residues 21-124 (9). This technique yielded only the average rate of hydrogen exchange for the S peptide but still allowed the establishment ofa number of highly protected protons and showed that their individual exchange rates must be very similar. Rosa and Richards (10, 11) extended the resolution of this method by performing rapid proteolytic digestion and separating the fragments ofthe enzyme by high-pressure liquid chromatography. They were able to assign individual rates to a number of hydr...

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“…In order to use the latter coordinates, a correction for water scattering was made by representing the scattering amplitude of a protein as the difference between the scattering amplitude of the molecule in vacuo and the scattering amplitude of the solution in the volume excluded by the molecule . The two scattering curves were the same for ribonuclease-A (Timchenko et al, 1978). For myoglobin, the differences observed could be ascribed to small structural changes (Fedorov and Denesyuk, 1978).…”

Section: Diffuse Scattering Studies Of Proteinsmentioning

confidence: 71%