Pfl bacteriophage

Orientational constraints have been collected for a wide variety of molecular systems from synthetic polymers [32, 33] to structural proteins, such as silk [34, 35]. Orientational constraints have also been collected for retinal bound to bacteriorhodopsin [36], suggesting a host of ligand receptor systems that might be studied. Orientational constraints have been collected on other synthetic and biosynthetic polypeptides in bilayer environments, such as Magainin-2, a toxin from frog skin [37], the M2 8 from the acetylcholine receptor [38] and M2-TMP from Influenza A virus [39]. Such studies have led to a description of the orientation of a-helices relative to the bilayer. Proteins such as the fd and Pfl bacteriophage coat proteins have also been... 

In a multidomain protein whose domains have fixed orientations relative to each other, a unique alignment tensor will represent the preferred orientation of all the domains in the anisotropic environment. Therefore, structure refinement with dipolar couplings is performed as in one-domain proteins (Sect. 8.4). Several examples are reported in the literature of cases with conformational ambiguity due to the lack of NOE contacts between the domains. One example is the determination of subdomain orientation of the riboso-mal protein S4 z)41 [97]. In this work the lack of NOE contacts between the domains produces an ambiguity in interdomain orientation. The authors use two different anisotropic media to obtain dipolar couplings (DMPC/DHPC bicelles and Pfl filamentous bacteriophages). They conclude that subdomain orientation in solution is similar to the one present in the crystal structure. 

Turner, R., and Weiner,J. (1993). Evaluation of transmembrane helix prediction methods using the recently defined NMR structures of the coat proteins from bacteriophages ml3 and pfl. Biochim. Biophys. Acta 1202, 161 — 168. 

Fig. 9. Comparison of the principal axis systems of alignment for the TAR RNA in bacteriophage Pfl as (A) experimentally determined and (B) predicted using the program SSIA.100...

L.133 Using two sets of backbone RDC data, collected in bacteriophage Pfl and bicelle media, they obtained order tensor parameters using a set of crystallographic coordinates for the structural model. This allowed the refinement of C -C bond orientations, which then provided the basis for their quantitative interpretation of C -H RDCs for 38 out of a possible 49 residues in the context of three different models. The three models were (A) a static xi rotameric state (B) gaussian fluctuations about a mean xi torsion and (C) the population of multiple rotameric states. They found that nearly 75% of xi torsions examined could be adequately accounted for by a static model. By contrast, the data for 11 residues were much better fit when jumps between rotamers were permitted (model C). The authors note that relatively small harmonic fluctuations (model B) about the mean rotameric state produces only small effects on measured RDCs. This is supported by their observation that, except for one case, the static model reproduced the data as well as the gaussian fluctuation model. 

Both X-ray and neutron fiber diffraction (as well as electron microscopy) techniques have been applied to filamentous viruses, for which the prospect of three-dimensional crystals is poor. By combining neutron and X-ray fiber diffraction, NMR, circular dichroism, and Raman and infrared spectroscopies, an atomic model for the filamentous bacteriophage Pfl has been derived (Liu and Day, 1994). Other studies concerning Pfl have relied on purely X-ray fiber diffraction data, together with molecular modeling, to provide detailed filament structures (Pederson et at, 2001 Welsh et at, 1998a,b, 2000). Eiber diffraction was also used to solve the structure of the rodlike helical tobacco mosaic virus (TMV), where all of the coat protein and three genomic nucleotides... 

A variety of weak liquid crystalline media have been used to align carbohydrates. Examples include Pfl phage,147-150 filamentous bacteriophage fd,151 C12E5/ -hexanol,77,152-154 C8E5/ -octanol,155 cetylpyridinium bromide / -hexanol /NaCl,73,156-158 DMPC/DHPC (dimyristoyl-phosphatidyl choline / dihexanoyl-... 

Schiksnis RA, Bogusky MJ, Tsang P, Opella SJ (1987) Structrue and dynamics of the Pfl filamentous bacteriophage coat protein in micelles. Biochemistry 26 1373-1381... 

Shon KJ, Kim Y, Colnago LA, Opella SJ (1991) NMR studies of the structure and dynamics of membrane-bound bacteriophage Pfl coat protein. Science 252 1303-1304... 

Side-chain C-C residual dipolar couplings have been measured by Vogeli et in uniformly deuterated and enriched human ubiquitin in the presence of bacteriophages Pfl by the use of the FLOPSY family experiment, one of the many broadband polarization transfer schemes. An excellent correlation between the measured RDCs and the 3D structure of the protein has been observed, indicating a potential use of the C-C RDCs in the structure determination of perdeuterated proteins. 

The atomic resolution structure of Pfl coat protein determined by solid-state NMR spectroscopy of magnetically aligned filamentous bacteriophage particles in solution has been compared to the structures previously determined by X-ray fiber and neutron diffraction. ... 

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