Spatial configuration of ribosomal proteins: A computer-generated model of the 30S subunit

Bollen, Alex; Cedergren, Robert; Sankoff, David; Lapalme, Guy

doi:10.1016/s0006-291x(74)80088-4

Biochemical and Biophysical Research Communications

1974

DOI: 10.1016/s0006-291x(74)80088-4

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Spatial configuration of ribosomal proteins: A computer-generated model of the 30S subunit

Alex Bollen

Robert Cedergren

David Sankoff

et al.

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1975

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Cited by 15 publications

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References 26 publications

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“…Curve. Theoretical curves of neutron scattering for some models of ribosomal protein topography proposed earlier by other au'thors (2)(3)(4)8) have been also calculated as described above and are presented in Fig. 6.…”

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confidence: 99%

“…From these and a number of less direct data, several models of the topography of ribosomal proteins in the 30S particle have been proposed (1)(2)(3)(4)(5)(6)(7)(8). Independently, the use of the immunoelectron microscopy technique has also led to two different models of the topography of ribosomal proteins on the surface of the 30S particle (9-12; see also ref.…”

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confidence: 99%

“…In recent years, the technique of chemical crosslinking of neighboring proteins by bifunctional reagents and measurements of the distances between deuterated or fluorescent-labeled proteins by using neutron scattering or energy transfer techniques, respectively, have contributed much to the knowledge of the protein topography in ribosomal particles and especially in the ribosomal 30S subunit of Escherichia coli. From these and a number of less direct data, several models of the topography of ribosomal proteins in the 30S particle have been proposed (1)(2)(3)(4)(5)(6)(7)(8). Independently, the use of the immunoelectron microscopy technique has also led to two different models of the topography of ribosomal proteins on the surface of the 30S particle (9-12; see also ref.…”

mentioning

confidence: 99%

“…I. M. Gelfand for giving us an excellent opportunity to discuss the paper at his Cell Biology Seminars at the Moscow State University. (2) Fi(F. 6 …”

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confidence: 99%

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Quaternary structure of the ribosomal 30S subunit: model and its experimental testing.

Spirin¹,

Serdyuk²,

Shpungin³

et al. 1979

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

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In considering the structure of the 30S subunit of the Escherichia coli ribosome, we have assumed that: (l) all or almost all the proteins within the 30S particle are compact and globular, as recently shown for the isolated proteins S4, S7, S8, S15, and S16 in solution [Serdyuk, I. N., Zaccai, G. & Spirin, A. S. (1978) In recent years, the technique of chemical crosslinking of neighboring proteins by bifunctional reagents and measurements of the distances between deuterated or fluorescent-labeled proteins by using neutron scattering or energy transfer techniques, respectively, have contributed much to the knowledge of the protein topography in ribosomal particles and especially in the ribosomal 30S subunit of Escherichia coli. From these and a number of less direct data, several models of the topography of ribosomal proteins in the 30S particle have been proposed (1)(2)(3)(4)(5)(6)(7)(8). Independently, the use of the immunoelectron microscopy technique has also led to two different models of the topography of ribosomal proteins on the surface of the 30S particle (9-12; see also ref. 13).However, two complications have hampered further progress. First, no information was available as to three-dimensional structure and morphology of the 16S RNA; this RNA is known to be a structural backbone for arrangement of ribosomal proteins. Second, immunoelectron microscopy (9, 10) and neutron scattering (14, 15) data on proteins within the 30S subunit, as well as some physical measurements of isolated ribosomal proteins (16-21), have suggested strongly elongated or very expanded shapes of many ribosomal proteins; this led to ambiguity in interpretation of the results on chemical crosslinking, energy transfer, etc.Most recently, a specific compact conformation of the 16S RNA has been visualized by electron microscopy (22). On the other hand, a number of ribosomal proteins, such as S4, S7, S8, S15, and S16, have been reinvestigated and found to be compact globular proteins with cooperative tertiary structures (23)(24)(25). Based on these new results and using the numerous data reported on mutual arrangement (topography) of ribosomal proteins, we have constructed a model of the quaternary structure of the ribosomal 30S particle and then checked it by neutron and x-ray scattering experiments.MODEL CONSTRUCTION Initial Assumptions. In constructing the model, we have adhered to the size and the asymmetric three-dimensional structure of the ribosomal 30S subunit first deduced by one of us from electron microscopy of freeze-dried and shadow-cast samples of the particles (26). Morphologically, the 30S particle was found to be subdivided into a "head," a "body," and a side "bulge" (Fig. 1). A similar subdivision of the 30S particles, with a side "platform," was reported also by Lake and Kahan (11) and Lake (27) on the basis of electron microscopy of negatively stained samples.We have proceeded from two principal assumptions: (i) RNA within the 30S particle has a specific V-like or Y-like conformation (Fig. 1), as it is visu...

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mentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

“…I. M. Gelfand for giving us an excellent opportunity to discuss the paper at his Cell Biology Seminars at the Moscow State University. (2) Fi(F. 6 …”

mentioning

confidence: 99%

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Quaternary structure of the ribosomal 30S subunit: model and its experimental testing.

Spirin¹,

Serdyuk²,

Shpungin³

et al. 1979

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

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“…Computer program Multidimensional scaling is a statistical technique that has been used for approximately 15 years in psychology and is now being used extensively in other fields, including an early attempt to generate a three-dimensional model of the 30S ribosome (19). It constructs a configuration of points in space from information about the distances between points.…”

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confidence: 99%

Use of computerized multidimensional scaling to compare immunoelectron microscopy data with protein near-neighbor information: application to the 30S ribosome from Escherichia coli.

Gaffney¹,

Craven²

1978

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

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A three-dimensional model of the protein arrangement in the Escherichia coli 30S ribosome was constructed by using computerized multidimensional scaling of immunoelectron microscope data. This enabled data comparison between the new electron microscope technique and other methods such as crosslinking, chemical protection, affinity labeling, energy transfer, and assembly interactions. The immunoelectron microscopy data are reasonably consistent with those from other sources. Reasons for some inconsistent data are discussed and our calculation of the dimensions of the proteins, both globular and elongated, are summarized. One of the most interesting recent developments in the analysis of ribosome structure is the use of immunoelectron microscopy (immuno-EM) to determine the relative positions of the individual proteins on the surface of the subunit particle (1)(2)(3)(4)(5) We have built such a model by using the following two-step procedure. First, a three-dimensional plaster model was made based on the immuno-EM diagrams of Tischendorf et al. (1, 2) and the antigenic sites were marked on its surface. Second, the shortest distances between all pairs of these antigenic sites were measured and used as input for a multidimensional scaling program. Its output gives the three-dimensional coordinates for a "naked" protein model-one without the outline of the ribosome. The model provides a unique and insightful view of the 30S ribosome. The uneven distribution of proteins within the subunit and the elongation of 12 of them are strikingly apparent. Questions on the relationship of structure to function take on fresh meaning but, more importantly, the model allows us to make a systematic comparison of all the relevant published data regarding protein-protein relationships.Computer program Multidimensional scaling is a statistical technique that has been used for approximately 15 years in psychology and is now being used extensively in other fields, including an early attempt to generate a three-dimensional model of the 30S ribosome (19). It constructs a configuration of points in space from information about the distances between points. For example, if a matrix were made of the 703 distances in miles between any 38 cities in the United States, and used as input in a multidimensional scaling program, the output would be 38 points representing the cities in the correct two-dimensional configuration. The orientation (north, south, east, west) would be left for the subjective decision of the user. Missing data and tied data can be accommodated but present some problems.The program places N points in a space of a given dimension so as to minimize STRESS, which measures the badness-of-fit between the configuration of points and the data. It represents the extent to which the data deviate in the least squares sense from the monotonic curve (see Fig. 3 A and B)

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Chemische Methoden zur Untersuchung der Ribosomenstruktur

Küchler¹

1976

Angewandte Chemie

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Spatial configuration of ribosomal proteins: A computer-generated model of the 30S subunit

Cited by 15 publications

References 26 publications

Quaternary structure of the ribosomal 30S subunit: model and its experimental testing.

Quaternary structure of the ribosomal 30S subunit: model and its experimental testing.

Use of computerized multidimensional scaling to compare immunoelectron microscopy data with protein near-neighbor information: application to the 30S ribosome from Escherichia coli.

Chemische Methoden zur Untersuchung der Ribosomenstruktur

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