Fraction of M protein bound to the plasma membrane [51] cond M ¼ 0.1 Attenuation factors [18, 19, 26, 27] / N / / P / / M / / G / / L ¼ 0.0 / 0.25 / 0.25 / 0.25 / 0.95 Degradation rate constants N protein [58] k dp,N ¼ 3.5 3 10 À5 sec À1 P protein [59] k dp,P ¼ 1.4 3 10 À6 sec À1 M protein [58] k dp,M ¼ 1.5 3 10 À4 sec À1 G protein b k dp,G ¼ 5.7 3 10 À5 sec À1 L protein [59] (if concentration P protein ! 10 3 concentration L protein ) k dp,L ¼ 1.2 3 10 À5 sec À1 (if concentration P protein , 10 3 concentration L protein ) k dp,L ¼ 4.3 3 10 À5 sec À1 mRNA [60] k d,mRNA ¼ 1.9 3 10 À4 s À1 nucleocapsid c k d,nc ¼ 1.9 3 10 À5 s À1 Host-dependent parameters Number of ribosomes in host cell [61] nrib ¼ 5 3 10 6 Elongation rate of ribosome [62] k e,rib ¼ 6 aa/s Spacing between neighboring ribosomes a (BHK/DBT) Srib ¼ 238. 5 Owing to their increased stability by encapsidation, nucleocapsids are less degradable than naked mRNAs. It was assumed that the nucleocapsids of VSV are degraded 10-fold slower than its mRNAs, and our simulation results were insensitive to this parameter. DOI: 10.1371/journal.pcbi/0020116.t001 detrimental for growth. For excessively large S cond , newly synthesized genomic nucleocapsids would tend to be prematurely incorporated into virion particles before they could serve as templates for transcription and replication. On the other hand, for extremely small S cond , genomic nucleocapsids would be utilized primarily to produce viral RNA without being packaged into viral progeny. Hence, an intermediate parameter value is expected to be optimal for viral growth. We estimated a possible range for the wild-type value of S cond by fitting our simulation results to previous experimental observations by others (2.5 3 10 À5 to 1.0 3 10 À4 , Figure S4 ). Our simulations further indicate that this range of S cond is near-optimal and optimal for VSV growth on BHK and DBT cells, respectively (unpublished data). Diversion and inhibition of host translation machinery create a time window of opportunity for translation of viral proteins. During the infection cycle, virus actively and passively competes with the host for limited translation resources by inhibiting host transcription and by amplifying viral mRNAs, respectively. Viral leader-mRNA and M protein play key roles in this inhibition [19, 28, [34] [35] [36] . As viral components accumulate in the cytoplasm from the initiation of infection, an ever-increasing fraction of host ribosomes are available for viral mRNAs ( Figure 3A , the fraction of ribosomes associated with viral mRNAs is defined by 1-rib_host in Equation 26 ). However, the inhibition of host macromolecular synthesis causes a failure to supply accessory factors needed for initiation and elongation steps of translation, resulting in a reduction in the fraction of active ribosomes over time ( Figure 3A , as described by f dec in Equation 25 ). These two mechanisms create a time window when active ribosomes are maximally available for viral translation in infected cells ( Figure 3A , refer to the term (1-rib_host)*f dec in Equation 27 ). The abundance of viral mRNAs and the limitation imposed by ribosomal spacing determine the fraction of the active ribosomes involved in translating viral mRNAs (occupied ribosomes in Figure 3B , refer to Equations 11 and 27) . In our model, if the occupied active ribosomes are less than the available ones (in this case the number of free active ribosomes . 0), viral translation is fully supported without any limitation of host machinery. In the early infection stages up to 7 h and 13 h post-infection for BHK and DBT cells, respectively, the host machinery is in excess ( Figure 3B ). However, at later times viral translation becomes limited by the host resources (in this case the number of free active ribosomes ¼ 0). This limitation may cause a transition from replication-dominant to assembly-dominant infection stages because the replication requires the continuous protein synthesis. As shown in Figure 3B , a small fraction of ribosomes as active forms (less than 5% out of 5 3 10 6 ribosomes, Table 1 ) are utilized for viral translation. Experiments and simulations of VSV gene-order mutants. For vaccine applications, one seeks to minimize viral pathogenicity and maximize its immunogenicity. Based on observed correlations between in vitro and in vivo results, we assume here that the pathogenicity and the immunogenicity of a virus are directly linked to the levels of progeny production [20, 37, 38] and G protein expression in infected cells [39, 40] , respectively. In the previous section we have showed that various VSV regulatory mechanisms are involved in maintaining balances, during infection, among viral synthesis processes, which indirectly indicates the importance of such balances for viral growth. Perturbations of such balances by genetic or genomic manipulations could provide ways to obtain viral phenotypes favorable to vaccine applications. We first test the predictive ability of our model by comparing simulated protein expression and growth of several gene-rearranged VSV strains with experimental results. Later we employ the model to predict how various genomic manipulations could attenuate virus growth and increase G protein expression.