Phage structure

Marvin, D.A. 1998. Filamentous phage structure, infection and assembly. Curr. Opin. Struct. Biol. 8, 150-158. 

Fig. 5.3 T-even phage structure before and after tail contraction.

See also Lactose Operon Regulation, Lac Repressor, Transcription Regulation in Phage, Structure of Cro and cl Repressors... 

Besides genes H and B, which code for phage structural proteins, and the genes involved in DNA replication (R, F, C, K, Q and P), the completion of 29 assembly requires genes I, L and D, coding for non-structural proteins. 

The number of helical turns in these structures is larger than those found so far in two-sheet p helices. The pectate lyase p helix consists of seven complete turns and is 34 A long and 17-27 A in diameter (Figure 5.30) while the p-helix part of the bacteriophage P22 tailspike protein has 13 complete turns. Both these proteins have other stmctural elements in addition to the P-helix moiety. The complete tailspike protein contains three intertwined, identical subunits each with the three-sheet p helix and is about 200 A long and 60 A wide. Six of these trimers are attached to each phage at the base of the icosahedral capsid. 

Figure 8.1 A region of DNA in the related bacteriophages lambda, 434, and P22 that controls the switch for synthesis of new phage particles. Two structural genes are involved in this switch one coding for a repressor protein and one coding for the Cro protein. Between these genes there is an operator region (OR) that contains three protein binding sites—ORl, OR2, and OR3.

These genetic experiments clearly demonstrated that the proposed structural model for the binding of these proteins to the phage operators was essentially correct. The second a helix in the helix-turn-helix motif is involved in recognizing operator sites as well as in the differential selection of operators by P22 Cro and repressor proteins. However, a note of caution is needed many other early models of DNA-protein interactions proved to be misleading, if not wrong. Modeling techniques are more sophisticated today but are still not infallible and are certainly not replacements for experimental determinations of structure. 

Mondragon, A., et al. Structure of the amino-terminal domain of phage 434 repressor at 2.0 A resolution. 

Since all members of this family of RNA phages have homologous coat proteins, their subunits are expected to have the same three-dimensional structure. It remains to be seen if the MS2 fold is also present in any other unrelated viruses. The fold is so far unique for the MS2 subunit, but similar structures have been observed in other proteins such as the major histocompatibility antigen, HLA, which was discussed in Chapter 15. 

How do the mutations identified by phage display improve binding specificity There is as yet no direct stmctural information on the phage-selected inhibitors however they can be modeled using data from the crystal structures of other Kunitz domains bound to serine proteinases. These studies lead to the conclusion that the mutations identified by phage display improve binding specificity by maximizing complementarity between the... 

EMPl, selected by phage display from random peptide libraries, demonstrates that a dimer of a 20-residue peptide can mimic the function of a monomeric 166-residue protein. In contrast to the minimized Z domain, this selected peptide shares neither the sequence nor the structure of the natural hormone. Thus, there can be a number of ways to solve a molecular recognition problem, and combinatorial methods such as phage display allow us to sort through a multitude of structural scaffolds to discover novel solutions. 

Structural scaffolds can be reduced in size while function is retained Phage display of random peptide librciries... 

Katz, B. A. (1997). Structural and mechanistic determinants of affinity and specificity of ligands discovered or engineered by phage display. Armu. Rev. Biophys. Biomol. Struct. 26, 27-45. 

The bacterial RNA viruses are all of quite small size, about 26 nm in size, and they are all icosahedral, with 180 copies of coat protein per virus particle. The complete nucleotide sequence of several RNA phages are known. In the RNA phage MS2, which infects Escherichia coli, the viral RNA is 3,569 nucleotides long. The virus RNA, although single stranded, has extensive regions of secondary and tertiary structure. The RNA strand in the virion has the plus (+) sense, acting directly as mRNA upon entry into the cell. 

The virus particle of phage T4 is structurally complex. It consists of an icosahedral head which is elongated by the addition of one or two extra bands of protein hexamers, the overall dimensions of the... 

Mainly the outer membrane ferrichrome receptor and transporter FhuA will be discussed because most structural and functional studies have been performed with this protein. In fact, FhuA was the first outer membrane protein identified (called TonA), with known functions as a phage and colicin receptor, that are related to iron transport (for a historical account, see Braun and Hantke 1977). 

Hermoso, J. A., Monterroso, B., Albert, A., Galan, B., Ahrazem, O., Garcia, P., Martinez-Ripoll, M., Garcia, J. L., and Menendez, M. (2003). Structural basis for selective recognition of pneumococcal cell wall by modular endolysin from phage Cp-1. Structure 11, 1239—1249. 

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