FFAS server: novel features and applications

Jaroszewski, Lukasz; Li, Zhanwen; Cai, Xueting; Weber, Christoph; Godzik, Adam

doi:10.1093/nar/gkr441

Cited by 142 publications

(129 citation statements)

References 39 publications

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“…Hence, we expect the TP901-1 MCP to exhibit a similar fold, and this is further supported by the detection of weak sequence similarity (but with high confidence) with the T7 and HK97 MCP sequences using the FFAS03 server and HHpred (Table 2) (26). A pseudoatomic model of the TP901-1 MCP shell was thus produced by rigid-body fitting of the icosahedral asymmetric unit of the mature HK97 capsid (Protein Data Bank [PDB] 1OHG) within the EM reconstruction (Fig.…”

Section: Resultsmentioning

confidence: 56%

Visualizing a Complete Siphoviridae Member by Single-Particle Electron Microscopy: the Structure of Lactococcal Phage TP901-1

Bebeacua

Lai

Vegge

et al. 2013

J Virol

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c Tailed phages are genome delivery machines exhibiting unequaled efficiency acquired over more than 3 billion years of evolution. Siphophages from the P335 and 936 families infect the Gram-positive bacterium Lactococcus lactis using receptor-binding proteins anchored to the host adsorption apparatus (baseplate). Crystallographic and electron microscopy (EM) studies have shed light on the distinct adsorption strategies used by phages of these two families, suggesting that they might also rely on different infection mechanisms. Here, we report electron microscopy reconstructions of the whole phage TP901-1 (P335 species) and propose a composite EM model of this gigantic molecular machine. Our results suggest conservation of structural proteins among tailed phages and add to the growing body of evidence pointing to a common evolutionary origin for these virions. Finally, we propose that host adsorption apparatus architectures have evolved in correlation with the nature of the receptors used during infection.

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Section: Resultsmentioning

confidence: 56%

Visualizing a Complete Siphoviridae Member by Single-Particle Electron Microscopy: the Structure of Lactococcal Phage TP901-1

Bebeacua

Lai

Vegge

et al. 2013

J Virol

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“…Both models were created using Jacakl as implemented in the Fold and Function Assignment System (FFAS) server (9), and then refined using the Relax protocol of Rosetta version 3.4 (10). On thousand models were generated for each initial model structure and then clustered using the Rosetta cluster protocol.…”

Section: Structure Modelingmentioning

confidence: 99%

D538G Mutation in Estrogen Receptor-α: A Novel Mechanism for Acquired Endocrine Resistance in Breast Cancer

et al. 2013

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Resistance to endocrine therapy occurs in virtually all patients with estrogen receptor a (ERa)-positive metastatic breast cancer, and is attributed to various mechanisms including loss of ERa expression, altered activity of coregulators, and cross-talk between the ERa and growth factor signaling pathways. To our knowledge, acquired mutations of the ERa have not been described as mediating endocrine resistance. Samples of 13 patients with metastatic breast cancer were analyzed for mutations in cancer-related genes. In five patients who developed resistance to hormonal therapy, a mutation of A to G at position 1,613 of ERa, resulting in a substitution of aspartic acid at position 538 to glycine (D538G), was identified in liver metastases. Importantly, the mutation was not detected in the primary tumors obtained prior to endocrine treatment. Structural modeling indicated that D538G substitution leads to a conformational change in the ligand-binding domain, which mimics the conformation of activated ligand-bound receptor and alters binding of tamoxifen. Indeed, experiments in breast cancer cells indicated constitutive, ligand-independent transcriptional activity of the D538G receptor, and overexpression of it enhanced proliferation and conferred resistance to tamoxifen. These data indicate a novel mechanism of acquired endocrine resistance in breast cancer. Further studies are needed to assess the frequency of D538G-ERa among patients with breast cancer and explore ways to inhibit its activity and restore endocrine sensitivity. Cancer Res; 73(23); 6856-64. Ó2013 AACR.

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“…However, more powerful similarity detection methods have been developed recently, which rely on profile-profile comparisons, such as HHpred (Hildebrand et al, 2009), HHblits (Remmert et al, 2012) HHalign (Biegert et al, 2006), FFAS (Jaroszewski et al, 2011) and WebPRC (Brandt & Heringa, 2009). In brief, a sequence profile is a representation of a multiple sequence alignment that contains information about which amino acids are 'tolerated' at each position of the alignment, and with which probability.…”

Section: Emaravirus P4 Mps Belong To the 30k Superfamilymentioning

confidence: 99%

Experimental and bioinformatic evidence that raspberry leaf blotch emaravirus P4 is a movement protein of the 30K superfamily

Chen

Karlin

et al. 2013

Journal of General Virology

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Emaravirus is a recently described genus of negative-strand RNA plant viruses. Emaravirus P4 protein localizes to plasmodesmata, suggesting that it could be a viral movement protein (MP). In the current study, we showed that the P4 protein of raspberry leaf blotch emaravirus (RLBV) rescued the cell-to-cell movement of a defective potato virus X (PVX) that had a deletion mutation in the triple gene block 1 movement-associated protein. This demonstrated that RLBV P4 is a functional MP. Sequence analyses revealed that P4 is a distant member of the 30K superfamily of MPs. All MPs of this family contain two highly conserved regions predicted to form b-strands, namely b1 and b2. We explored by alanine mutagenesis the role of two residues of P4 (Ile106 and Asp127) located in each of these strands. We also made the equivalent substitutions in the 29K MP of tobacco rattle virus, another member of the 30K superfamily. All substitutions abolished the ability to complement PVX movement, except for the I106A substitution in the b1 region of P4. This region has been shown to mediate membrane association of 30K MPs; our results show that it is possible to make non-conservative substitutions of a well-conserved aliphatic residue within b1 without preventing the membrane association or movement function of P4.

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FFAS server: novel features and applications

Cited by 142 publications

References 39 publications

Visualizing a Complete Siphoviridae Member by Single-Particle Electron Microscopy: the Structure of Lactococcal Phage TP901-1

Visualizing a Complete Siphoviridae Member by Single-Particle Electron Microscopy: the Structure of Lactococcal Phage TP901-1

D538G Mutation in Estrogen Receptor-α: A Novel Mechanism for Acquired Endocrine Resistance in Breast Cancer

Experimental and bioinformatic evidence that raspberry leaf blotch emaravirus P4 is a movement protein of the 30K superfamily

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