Chapter 7

Ribosomal Proteins and Their Structural Transitions on and off the Ribosome

Salam Al-Karadaghi

Salam Al-Karadaghi

Molecular Biophysics, Center of Chemistry and Chemical Engineering, Lund University, Box 124, SE-221 00 Lund, Sweden

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Natalia Davydova

Natalia Davydova

Molecular Biophysics, Center of Chemistry and Chemical Engineering, Lund University, Box 124, SE-221 00 Lund, Sweden

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Irina Eliseikina

Irina Eliseikina

Molecular Biophysics, Center of Chemistry and Chemical Engineering, Lund University, Box 124, SE-221 00 Lund, Sweden

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Maria Garber

Maria Garber

Institute of Protein Research, Russian Academy of Sciences, 142292 Pushchino, Moscow Region, Russia

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Anders Liljas

Anders Liljas

Molecular Biophysics, Center of Chemistry and Chemical Engineering, Lund University, Box 124, SE-221 00 Lund, Sweden

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Natalia Nevskaya

Natalia Nevskaya

Institute of Protein Research, Russian Academy of Sciences, 142292 Pushchino, Moscow Region, Russia

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Stanislav Nikonov

Stanislav Nikonov

Institute of Protein Research, Russian Academy of Sciences, 142292 Pushchino, Moscow Region, Russia

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Svetlana Tishchenko

Svetlana Tishchenko

Institute of Protein Research, Russian Academy of Sciences, 142292 Pushchino, Moscow Region, Russia

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First published: 27 March 2000

Summary

This chapter briefly reviews the structural data available, identifies similarities and differences, and illustrates some difficulties in using the structures of isolated components for insertion into the structures of whole ribosomes or subunits determined at lower resolution. An awareness of the possible differences in structure is necessary for an appreciation of the usefulness of structural studies of isolated components from a larger system such as the ribosome. The fraction of ribosomal proteins that has been structurally characterized is now more than one-third of all ribosomal proteins from bacteria. The chapter focuses on the domain arrangement of ribosomal proteins, and structural motifs. The extended conformations of some ribosomal proteins can be compared to proteins like calmodulin, which has a very elongated structure in one state while the α-helix that separates the two domains becomes bent in another state, with the effect that the protein adopts a more globular structure. L1 is a two-domain protein. The structure of L1 from Thermus thermophilus shows the two domains in close contact. Domain II can be described as an insert in domain I. Thus, there are two connections between the domains. The structural investigations have clearly established that the ribosomal proteins are formed by stable domains with significant hydrophobic cores that would hardly alter their structures upon binding to the ribosome. Several ribosomal proteins are built of two or more domains, sometimes with significant flexibility between them. Long, more or less flexible loops also frequently occur in ribosomal proteins.

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