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Chapter 8 : Structures of Bacterial Ribosomal Proteins: High-Resolution Probes of the Architecture and Mechanism of the Ribosome

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Abstract:

It has long been recognized that a complete understanding of the mechanism of translation ultimately depends on determining the molecular structure of the ribosome. The past 4 years have seen a number of exciting advances in ribosome research, and this daunting task is now considered a real possibility. This chapter summarizes the findings of the researchers from the past 4 years. The four ribosomal proteins, S4, S7, S8, and S15, together with S17, control the initial stages of the folding of the 16S rRNA molecule and are crucial determinants of the 30S architecture. There are two putative RNA binding sites located on S8. The first is located at the top of the N-terminal domain at the C-terminal end of helix α1 and is flanked by regions of positive potential. The second site is on the lower surface of the C-terminal domain. The overall dumbbell-shaped architecture of the putative S15 RNA binding surface suggests that the protein may interact with two adjacent RNA sites. Steadily accumulating biochemical and biophysical data have increased one’s understanding of the structure and mechanism of the bacterial ribosome, and contemporary data have been used periodically to construct models of the subunits, which then form the basis for subsequent experimentation. The chapter describes the pertinent information that are identified for each of the protein structures determined during the past 7 years.

Citation: White S, Clemons, Jr. W, Davies C, Ramakrishnan V, Wimberly B. 2000. Structures of Bacterial Ribosomal Proteins: High-Resolution Probes of the Architecture and Mechanism of the Ribosome, p 73-84. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch8

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Figures

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Figure 1

Structure of ribosomal protein S4 from . (a) Cartoon showing locations of the -helices (orange), -strands (yellow), and loops (yellow). The N and C termini are indicated. (b) Locations of functionally and biochemically important amino acids. Blue, putative RNA binding residues; magenta, conserved surface hydrophobic residues; red, site of point mutation conferring a phenotype. (c) Surface charge potential as calculated by the program GRASP ( ). Blue, positive; red, negative; white, hydrophobic.

Citation: White S, Clemons, Jr. W, Davies C, Ramakrishnan V, Wimberly B. 2000. Structures of Bacterial Ribosomal Proteins: High-Resolution Probes of the Architecture and Mechanism of the Ribosome, p 73-84. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch8
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Image of Figure 2
Figure 2

Structure of ribosomal protein S7 from . (a) Cartoon showing locations of -helices (orange), -strands (yellow), and loops (yellow). The N and C termini are indicated. (b) Locations of functionally and biochemically important amino acids. Blue, putative RNA binding residues; magenta, conserved surface hydrophobic residues; green, residue cross-linked to RNA. (c) Surface charge potential as calculated by the program GRASP ( ). Blue, positive; red, negative; white, hydrophobic.

Citation: White S, Clemons, Jr. W, Davies C, Ramakrishnan V, Wimberly B. 2000. Structures of Bacterial Ribosomal Proteins: High-Resolution Probes of the Architecture and Mechanism of the Ribosome, p 73-84. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch8
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Image of Figure 3
Figure 3

Structure of ribosomal protein S8 from . (a) Cartoon showing locations of -helices (orange), -strands (yellow), and loops (yellow). The N and C termini are indicated. (b) Locations of functionally and biochemically important amino acids. Blue, putative RNA binding residues; magenta, conserved surface hydrophobic residues; green, residue cross-linked to RNA (bottom right) and ribosomal protein S5 (top left). (c) Surface charge potential as calculated by the program GRASP ( ). Blue, positive; red, negative; white, hydrophobic

Citation: White S, Clemons, Jr. W, Davies C, Ramakrishnan V, Wimberly B. 2000. Structures of Bacterial Ribosomal Proteins: High-Resolution Probes of the Architecture and Mechanism of the Ribosome, p 73-84. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch8
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Image of Figure 4
Figure 4

Structure of ribosomal protein S15 from . (a) Cartoon showing locations of -helices (orange) and loops (yellow). The N and C termini are indicated. Note that the N-terminal helix belongs to a neighbor in the unit cell, but its location on the molecule appears to be correct. (b) Locations of putative RNA binding residues (blue). (c) Surface charge potential as calculated by the program GRASP ( ). Blue, positive; red, negative; white, hydrophobic.

Citation: White S, Clemons, Jr. W, Davies C, Ramakrishnan V, Wimberly B. 2000. Structures of Bacterial Ribosomal Proteins: High-Resolution Probes of the Architecture and Mechanism of the Ribosome, p 73-84. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch8
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