Molecular Structure of fd (f1, M13) Filamentous Bacteriophage Refined with Respect to X-ray Fibre Diffraction and Solid-state NMR Data Supports Specific Models of Phage Assembly at the Bacterial Membrane

Marvin, D.A.; Welsh, Liam; Symmons, Martyn F.; Scott, Walter R. P.; Straus, Suzana K.

doi:10.1016/j.jmb.2005.10.048

Cited by 125 publications

(146 citation statements)

References 81 publications

Supporting

Mentioning

131

Contrasting

Unclassified

Order By: Relevance

“…After forming methacrylamide 2 by using methacrylic anhydride in alkaline media and a series of N-(3-dimethylaminopropyl)-NЈ-ethylcarbodiimide (EDC)-mediated amide bond formation and deprotection steps, reaction of the terminal amine of 4 with N-succinimidyl-3-maleimidobutyrate afforded 6 in 8.4% overall yield over six steps. The pVIII major coat protein of wild-type bacteriophage was chemically modified with Traut's reagent at the single exposed lysine residue on the outside of the phage coat (Lys 8 ) (12). Addition of monomer 6 allowed for facile modification of the phage surface through Michael addition of the thiol to the maleimide of 6, effectively creating a macromonomer suitable for free-radical polymerizations (Fig.…”

Section: Resultsmentioning

confidence: 99%

Biologically templated organic polymers with nanoscale order

Willis¹,

Eubanks²,

Wood³

et al. 2008

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

View full text Add to dashboard Cite

Methods for the construction of ordered nanoscale arrays have been implicated in fields ranging from separation technologies to microelectronics. Yet, despite the plethora of nanoscale structures assembled in nature that use a templating strategy, chemists have been unable to replicate this success. A technology is reported for templated organic polymers composed of filamentous bacteriophage-polyacrylamide biomacromolecules that self-assemble into highly ordered helical bundles displaying hexagonal close packing. The results align with a previously reported mathematical prediction for the close packing of flexible tubes. This biopolymeric assembly can be viewed as a magnification of the inherent microscopic chirality and helicity present in individual phage particles at the macroscale level.bacteriophage ͉ nanopores ͉ polyacrylamide N ature synthesizes a large repertoire of highly ordered nanoscale structures from a limited subset of molecules. However, chemists have not matched this success even though a much larger set of reagents and reactions are available at their disposal. This is particularly evident for organic polymers where construction of materials with ordered nanopores remains elusive (1). In many instances, nature's main device to overcome the inherent entropic barrier for assembly is the use of a template to preorganize an array of chemicals that react to form biological polymers such as nucleic acids and proteins. Ultimately, nanoscale assemblies are formed from homologous or heterologous sets of these polymers. We reasoned that similarly ordered organic polymers could be biomimetically prepared by using a templating approach. Filamentous bacteriophage M13 was chosen as a template given that such virions can form liquid crystals and ordered two-dimensional films (2, 3). Structurally, bacteriophage M13 is a rigid helical rod Ϸ930 nm in length and 6.5 nm in diameter. The shaft of the rod consists of Ϸ2,700 copies of a single helical protein (pVIII) of 50 aa where one end contains five copies of a protein critical for binding to the bacterial cell host (pIII) and the other end contains five copies of two different proteins (pVII and pIX) consisting of 33 aa and 32 aa, respectively. All of these proteins can be used to express large numbers of antibodies and peptides on the phage surface (4). By using this strategy, we now report a technology for templated organic polymers composed of filamentous bacteriophage-polyacrylamide biomacromolecules that self-assemble into highly ordered helical bundles displaying classical hexagonal close packing with remarkable physical properties. Results and DiscussionAlthough protein-polymer bioconjugates are widespread in drug development, their use in the design of new materials is much less common. The traditional approach to the preparation of protein-polymer bioconjugates has been the coupling of two macromolecules postpolymerization. In such cases, the polymer is activated with amine-or thiol-reactive functional groups for reaction with such amino acids as lysine...

show abstract

Section: Resultsmentioning

confidence: 99%

Biologically templated organic polymers with nanoscale order

Willis¹,

Eubanks²,

Wood³

et al. 2008

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

View full text Add to dashboard Cite

show abstract

“…They consist of a single-stranded circular DNA packed in a tube composed of the major coat protein pVIII (98% by mass), and a few copies of the minor coat proteins capping the ends of the phage particle (reviewed in [8,9]). …”

Section: Phage As Bioselective Nanomaterialsmentioning

confidence: 99%

“…About half of amino acids are exposed, while another half is buried in the capsid (shown as red in A). The model was built by Dr. Alexey M. Eroshkin using Marvin's phage model [8]. TEM micrograph of bacteria-phage complex.…”

Section: Figmentioning

confidence: 99%

Landscape phage as a molecular recognition interface for detection devices

Petrenko

2008

Microelectronics Journal

View full text Add to dashboard Cite

Filamentous phages are thread-shaped bacterial viruses. Their outer coat is a tube formed by thousands equal copies of the major coat protein pVIII. Libraries of random peptides fused to pVIII domains were used for selection of phages probes specific for a panel of test antigens and biological threat agents. Because the viral carrier in the phage borne bio-selective probes is infective, they can be cloned individually and propagated indefinitely without needs of their chemical synthesis or reconstructing. As a new bioselective material, landscape phages combine unique characteristics of affinity reagents and self assembling proteins. Biorecognition layers formed by the phage-derived probes bind biological agents with high affinity and specificity and generate detectable signals in analytical platforms. The performance of phage-derived materials as biorecognition interface was illustrated by detection of Bacillus anthracis spores and Salmonella typhimurium cells. With further refinement, the phage-derived analytical platforms for detecting and monitoring of numerous threat agents may be developed, since phage interface against any bacteria, virus or toxin may be readily selected from the landscape phage libraries. As an interface in the field-use detectors, they may be superior to antibodies, since they are inexpensive, highly specific and strong binders, resistant to high temperatures and environmental stresses.

show abstract

“…Bacteriophage fd (which differs from the widely used M13 by only a single amino acid) has a very small capsid protein containing only 50 residues. The main techniques that have been used previously to generate models for the subunit structure and packing have been x-ray fiber diffraction [29] and solid-state NMR [30]. However, these models have differed considerably, and now we have two different EM reconstructions [28] that cannot be reconciled with either the x-ray or the NMR models.…”

Section: Structural Heterogeneitymentioning

confidence: 99%

“…However, these models have differed considerably, and now we have two different EM reconstructions [28] that cannot be reconciled with either the x-ray or the NMR models. It was recently shown [29] that the same NMR constraints used to generate the NMR model could also be satisfied by the x-ray fiber diffraction model, suggesting that the NMR constraints were not sufficient to generate a unique model. On the other hand, it has been known that due to the cylindrical averaging and overlap of different Bessel functions in x-ray fiber diffraction, models derived from this technique may not be unique, either.…”

Section: Structural Heterogeneitymentioning

confidence: 99%

Single-particle reconstruction from EM images of helical filaments

Egelman

2007

Current Opinion in Structural Biology

View full text Add to dashboard Cite

SummaryHelical filaments were the first structures to be reconstructed in three-dimensions from electron microscopic images, and continue to be extensively studied due to the large number of such helical polymers found in biology. In principle, a single image of a helical polymer provides all of the different projections needed to reconstruct the three-dimensional structure. Unfortunately, many helical filaments have been refractory to the application of traditional (Fourier-Bessel) methods due to variability, heterogeneity and weak scattering. Over the past several years many of these problems have been surmounted using single-particle type approaches that can do substantially better than Fourier-Bessel approaches. Applications of these new methods to viruses, actin filaments, pili and many other polymers show the great advantages of the new methods.

show abstract

Molecular Structure of fd (f1, M13) Filamentous Bacteriophage Refined with Respect to X-ray Fibre Diffraction and Solid-state NMR Data Supports Specific Models of Phage Assembly at the Bacterial Membrane

Cited by 125 publications

References 81 publications

Biologically templated organic polymers with nanoscale order

Biologically templated organic polymers with nanoscale order

Landscape phage as a molecular recognition interface for detection devices

Single-particle reconstruction from EM images of helical filaments

Contact Info

Product

Resources

About