administration of an antibody ( natalizumab ) to the alpha 4 integrin molecule binding site to the head region of the vascular cell adhesion molecule 1 ( vcam-1 ) molecule was found to be associated with systemic jc viremia and subsequent progressive multifocal leukoencephalopathy ( pml ) in a 60 year old crohn s disease patient who had been previously treated with infliximab and azothioprine . after only 6 administrations of the natalizumab antibody , serum jc viral load rose from being undetectable to 520 copies / ml and then to 6600 dna copies / ml two months later when pml was suspected , and required brain biopsy for diagnosis ; up to 3.9 million jc virus dna copies per brain glial cell were found . since the exact cause of the jc viremia remains unclear in this case , the future therapeutic role for natalizumab in treating multiple sclerosis and other disorders remains uncertain . to help understand the pathogenesis of antibody related jc viremia and subsequent pml , it is hypothesized here that the alpha 4 integrin antibody may disrupt the peripheral binding of the virus in natural tissue reservoirs in certain individuals ; jc viremia after blockade of the normal alpha 4 integrin binding sites for the virus in lymphoid tissue such as spleen and the tonsils could overwhelm the normal cytotoxic t cell immune surveillance defense mechanisms . indirect support for this hypothesis of peripheral binding of vp1 to alpha 4 integrin in lymphoid tissue comes from the work of caruso et al . who found an important vp1 receptor function for the alpha 4 integrin molecule , which like the beta 1 integrin molecule is heavily glycosylated with terminal sialic acid residues , which were already known to mediate vp1 attachment . this study therefore attempts to identify critical amino acid binding sequences that may mediate an interaction between alpha 4 integrin molecules in normal host tissue and the jc virus vp1 coat proteins . since idsp is a critical vcam-1 amino acid sequence for binding to the alpha 4 integrin , a search was made to find a similar sequence in the vp1 protein that could mediate an attachment to integrins . using accession number j02288.1 , the protein sequence for the polyoma vp1 coat protein was analyzed for idsp sequences using the national center for biotechnology information on - line data base ( on - line web address : http://www.ncbi.nlm.nih.gov/ ) . enumeration of the amino acid residues followed the convention of numbering vp1 residues after the initial met residue ( caruso et al . ) . alignment information for different strains of polyoma virus was analyzed by a conserved domain search at the following on - line web address : http://www.ncbi.nlm.nih.gov/structure/cdd/wrpsb.cgi . the localization of the dsp sequence for the human polyoma vp1 protein was studied using the molecular modeling database ( mmdb ) , which enables reconstruction and interactive viewing of the three dimensional macromolecular structures with cn3d software ; web address : http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=structure the individual vp1 protein structure was analyzed as well as one of the 72 pentameric icosahedral capsids that cover the surface of the polyoma virus , and visualized in relation to hydrophobicity as well as charge . although the full idsp sequence was not found , a dsp sequence was found for the jc polyoma virus vp1 coat protein ( accession number p03089 ) as well as mouse polyomavirus ( strain p16 small - plaque ; accession - number 1sie_a ) , as well as chain 1 , simian virus 40 ( accession number 1sva_1 ) , but not for kilham polyomavirus ( accession number p24595 ) , budgerigar fledgling polyomavirus ( bfpyv ; accession number p13891 ) , hamster polyomavirus ( hapyv ; accession number p03092 ) , african green monkey polyomavirus ( accession number p04010 ) , or bovine polyomavirus ( accession number p24848 ) . alligned short segments of vp1 which display the homologous dsp sequence are shown in red in figure 1 with residues 70,71 , and 72 for the jc polyoma virus being aspartic acid ( d ) , serine ( s ) , and proline ( p ) respectively . the three dimensional external view of a single pentamer capsid ( figure 2 ) reveals accessible dsp residues for interaction and potential ligand binding . a detailed interactive review of a ball and stick type model ( figure 3 ) one of the five individual molecules that form a pentamer suggests a peripheral location to the dsp loop in relation to the bulk of the vp1 molecule , with the suggestion that a pocket is formed by this eccentric peripheral loop that could allow insertion of a small ligand molecule into this site . although the full idsp sequence was not found , a dsp sequence was found for the jc polyoma virus vp1 coat protein ( accession number p03089 ) as well as mouse polyomavirus ( strain p16 small - plaque ; accession - number 1sie_a ) , as well as chain 1 , simian virus 40 ( accession number 1sva_1 ) , but not for kilham polyomavirus ( accession number p24595 ) , budgerigar fledgling polyomavirus ( bfpyv ; accession number p13891 ) , hamster polyomavirus ( hapyv ; accession number p03092 ) , african green monkey polyomavirus ( accession number p04010 ) , or bovine polyomavirus ( accession number p24848 ) . alligned short segments of vp1 which display the homologous dsp sequence are shown in red in figure 1 with residues 70,71 , and 72 for the jc polyoma virus being aspartic acid ( d ) , serine ( s ) , and proline ( p ) respectively . the three dimensional external view of a single pentamer capsid ( figure 2 ) reveals accessible dsp residues for interaction and potential ligand binding . a detailed interactive review of a ball and stick type model ( figure 3 ) one of the five individual molecules that form a pentamer suggests a peripheral location to the dsp loop in relation to the bulk of the vp1 molecule , with the suggestion that a pocket is formed by this eccentric peripheral loop that could allow insertion of a small ligand molecule into this site . as reported in preliminary form by meyer , a dsp sequence has now been found that may represent a alpha 4 integrin binding site for the major jc polyoma virus external coat protein known as vp1 . since the idsp sequence is critical in binding vcam-1 to the alpha 4 integrin molecule , and since the alpha 4 integrin molecule is also thought to serve as a post - attachment receptor for vp1 , it is possible that that antibodies to the alpha 4 integrin molecule leaves the virus in peripheral lymphoid tissue in a free and unbound state . since the alpha 4 integrin antibody natalizumab is associated with jc viremia and subsequent overwhelming brain infection by the virus ( pml ) , it is hypothesized that alpha 4 integrin molecules in lymphoid tissue normally binds to the jc virus vp1 protein to render it non - infective by successfully competing with other receptors for the virus . the binding may be mediated by the dsp motif at residues 70,71 , and 72 for jc , and at 88,89,90 for the murine polyoma a2 strain ; for the latter , a nearby critical arginine residue at position 77 governs infectivity of the virus and is believed to bind to sialic acid containing molecules such as integrins . it is unclear if dsp mediated binding of vp1 to the alpa 4 integrin integrin molecule produces secondary conformational changes at the nearby vp1 arginine 77 sialic acid binding site to alter infectivity of the virus . extensive literature exists regarding other viruses that display specific binding to integrins ; antibodies to specific integrins can prevent infection by specific cytopathic viruses that normally do not show the jc phenomenon of long term benign persistence and dormancy within tissue . the alpha 6 integrin likely serves as a cellular receptor for papillomaviruses , whereas the alpha 5 beta 6 integrin binds to cocksackie virus a9 through a rgd amino acid sequence ; this sequence is also implicated in the binding of b cell lymphotropic polyoma virus capsids to the alphav beta 3 integrin . when the alphav is found in combination with beta 8 , this integrin can serve as a receptor for the foot and mouth disease virus ; when alphav combines with beta 1 , the integrin molecule dimer can be a receptor for the adenovirus . the alphav integrin is particularly important , as other combinations yield different viral specificities : when combined with beta 3 , the integrin dimer can bind the west nile virus , cytomegalovirus , as well as rotavirus . regarding the kaposi s sarcoma - associated herpesvirus , viral entry infectivity seems to depend on binding to inactive , bent , alphavbeta3-integrin molecules at a specific bend site at the plexin - semaphorinintegrin ( psi ) , where molecular motion could otherwise take place to straighten the molecule into an active form . further research is needed to understand if alpha 4 integrin binding to the dsp sequence of vp1 normally leaves the jc virus in a non - infective state . successful competition with other tissue receptors for the virus might be an adequate explanation for why the jc virus can found in normal tissue of over 70% of normal individuals without causing pml , which is extremely rare in fully immunocompetent individuals , yet linked to pml in up to 4 to 6% of immunosuppressed hiv infected patients . in vitro studies are needed as well to test if synthetic dsp sequences can inhibit binding of vp1 to alpha 4 integrin molecules ; should such an interaction be documented , it may have relevance to the understanding the natural biology of the jc polyoma virus , which can remain non - infective in not only kidney and lymphoid tissue , but also even the brain . further understanding of how the jc virus persists is important in understanding multiple disease states , including primary brain tumors , which have been found to harbor the virus and express t antigens in oligodendrogliomas . this study has limitations in that the key publications by caruso et al . which found a viral vp1 protein receptor function for the alpha 4 integrin molecule , derived their research findings from the murine polyoma virus ; however , like the beta 1 integrin molecule and the serotonin receptor molecule , the alpha 4 integrin molecule is heavily glycosylated with terminal sialic acid residues . it is important to also note that blockade of the serotonin receptor 2a by risperidone does not inhibit jcv attachment , internalization and replication in primary human fetal glial cells , raising questions about the biologic relevance about data concerning the serotonin receptor also serving as a proposed receptor for the jc virus in light of the well established role for integrin molecules as receptors for other viruses ; furthermore , linear sialylated pentasaccharides with the sequence neunac-2,6-gal-1,4-glcnac-1,3-gal-1,4-glc present on host glycoproteins and glycolipids have now been found to serve as a specific jcv recognition motif  future research is needed to understand how this applies to integrin alpha 4 terminal oligosaccharide sequences . finally , it is important to point out that caution with the use of natalizumab is strongly advised , as the latest data has revealed an incidence rate of 212 confirmed cases of pml among 99,571 patients treated with natalizumab , equating to 2.1 cases per 1000 treated patients .
the jc polyoma viral coat protein vp1 was analyzed for amino acid sequences homologies to the idsp sequence which mediates binding of vla-4 ( integrin alpha 4 ) to vascular cell adhesion molecule 1 . 
 although the full sequence was not found , a dsp sequence was located near the critical arginine residue linked to infectivity of the virus and binding to sialic acid containing molecules such as integrins ( 3 ) . for the jc polyoma virus , 
 a dsp sequence was found at residues 70 , 71 and 72 with homology also noted for the mouse polyoma virus and sv40 virus . 
 three dimensional modeling of the vp1 molecule suggests that the dsp loop has an accessible site for interaction from the external side of the assembled viral capsid pentamer .