Simulation of HIV-1 Molecular Evolution in Response to Chemokine Coreceptors and Antibodies - Immunoinformatics - page 164

Fig. 3. Twenty randomly chosen V3 sequences from one replicate simulation with a selection
coefficient scaling constant of 0.25. Other parameter values are as described in Fig. 2. Periods
indicate identity with the initial sequence.
9.4.3 Adaptation to Antibody Surveillance
Parameter values for the logistic growth equation (Eq. (1)), used to model affinity
maturation, were chosen to give realistic antibody response dynamics. The affinity of
antibody to hapten increases up to 10,000-fold (Wedemayer, Patten, Wang, Schultz,
and Stevens 1997), but increases only up to 1000-fold for a protein immunogen
(lysozyme) (Cauerhff, Goldbaum, and Braden 2004), and affinity increases of only
around 100-fold have been reported in response to HIV-1 gp120 (Toran, Kremer,
Sanchez-Pulido, de Alboran, del Real, Llorente, Valencia, de Mon, and Martinez
1999). Therefore, it was assumed that a 1000-fold increase in affinity is the maxi-
mum in response to a protein immunogen. Setting the maximum affinity ( K ) to 1.0