E-scores were calculated for each of the M-recombinants and their corresponding sets of S-recombinant proteins and a permutation test was performed which counted the fraction of times that the sum of E-scores for the set of real M-recombinant proteins were less than the sum of E-scores for each of 100,000 sets of S-recombinant proteins. This fraction corresponds to the p-value that the real recombination events that are DS-437 collectively represented amongst all the M-recombinants are not collectively less disruptive of protein folding than are those represented amongst their corresponding sets of S-recombinants: For a particular gene a p-value,0.05 therefore suggests.95% confidence that recombination events detectable under natural conditions within that gene are less disruptive of protein folding than would be expected in the absence of either selection disfavoring the survival of viruses that express chimaeric proteins with disrupted folds or mechanistic factors that cause recombination events to occur most frequently at genomic sites where they will have minimal TM5275 sodium salt impact on protein folding. Recombination that occurs between divergent genome fragments having largely independent evolutionary histories can potentially disrupt coevolved intra-genome interactions such as those occurring between amino acids within three-dimensional protein folds. Here chimaeric proteins resembling those expressed by actual viruses were computationally tested to determine whether they displayed lower degrees of predicted folding disruption than those of randomly generated protein chimaeras. Actual recombinants sampled from nature would be expected to display less disruption of intra-protein interactions than simulated recombinants either if natural selection disfavoured the survival of recombinants expressing misfolded proteins, or recombination breakpoints tended to coincidentally occur most frequently at sites where they would have minimal impact on protein folding. Figure 2A illustrates degrees of intra-protein amino-acid �C amino-acid interaction disruption that are predicted to occur within various HIV-1 proteins between HIV variants that have previously been observed to recombine.