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1

MOFOID - not only the protein modeling server.

100%

Szczesny P., Wieczorek G., Zielenkiewicz P.

Acta Biochimica Polonica

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2005

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vol. 52

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issue 1

267-269

EN

MOFOID is a new server developed mainly for automated modeling of protein structures by their homology to the structures deposited in the PDB database. Selection of a template and calculation of the alignment is performed with the Smith-Waterman or Needleman-Wunsch algorithms implemented in the EMBOSS package. The final model is built and optimised with programs from the JACKAL package. The wide spectrum of options in the web-based interface and the possibility of uploading user's own alignment make MOFOID a suitable platform for testing new approaches in the alignment building. The server is available at https:// valis.ibb.waw.pl/mofoid/.

2

Homologues of HSV-1 nuclear egress factor UL34 are potential phosphoinositide-binding proteins

61%

Wyrwicz L. S., Koczyk G., Rychlewski L.

Acta Biochimica Polonica

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2008

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vol. 55

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issue 1

207-213

EN

During the herpesvirus replication cycle, viral transcription, DNA replication, formation of capsids and DNA packaging occur in the nucleus. The subsequent nuclear egress of newly synthesized nucleocapsids is performed by budding of the inner leaflet of the nuclear membrane, which creates the primary envelope. Although products of two genes conserved throughout the Herpesviridae family (HSV-1 UL34 and UL31) have previously been shown to be involved in the execution of this process, the molecular basis of their activity is not clear. Here we present results of protein structure prediction for the conserved domain of UL34. The applied methodology suggests that this protein adopts a pleckstrin homology (PH) fold to perform its function. A detailed inspection of the ligand binding site strongly supports the hypothesis that UL34 orthologs can recognize phosphoinositides. Since previous works suggest that alterations of UL34 gene product result in a drastic impairment of primary envelopment of HSV-1 and trapping of capsids in the nucleus, the presented data may lead to the development of novel anti-herpetic therapeutic strategies where analogs of phosphoinositides are administered.

3

Cytomegalovirus immediate early gene UL37 encodes a novel MHC-like protein

61%

Wyrwicz L. S., Rychlewski L.

Acta Biochimica Polonica

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2008

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vol. 55

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issue 1

67-74

EN

The cytomegalovirus (CMV) genome encodes four clusters of genes expressed immediately after infection - i.e.: UL36-38, UL122-123, TRS1-IRS1, and US3. The general function of these genes is associated with inhibition of cellular mechanisms of antiviral response. Although several biological processes have been mapped onto specific gene products, the knowledge of the molecular mechanism of their activity remains fragmentary. Here, we report the application of protein structure prediction methods in assigning the function to a glycosylated domain encoded by UL37 of CMV (gpUL37, UL37x3). The discerned similarity clearly points out that this domain represents a novel type of a major histocompatibility complex (MHC)-like protein, and consequently may play a central role in an additional mechanism of escape from antiviral response.

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3 Acta Biochimica Polonica

2 2008

1 2005

2 Rychlewski L.

2 Wyrwicz L. S.

1 Koczyk G.

1 Szczesny P.

1 Wieczorek G.

1 Zielenkiewicz P.

MOFOID - not only the protein modeling server.

Homologues of HSV-1 nuclear egress factor UL34 are potential phosphoinositide-binding proteins

Cytomegalovirus immediate early gene UL37 encodes a novel MHC-like protein