We have performed molecular dynamics simulations of protein surface loops solvated by explicit water,where a prime focus of the study is the small numbers (e.g.,approx 100) of explicit water molecules employed.The models include only part of the protein (typically 500-1000 atoms),and the water molecules are restricted to a region surrounding the loop.In this study,the number of water molecules (N_w) is systematically varied,and convergence with a large N_w is monitored to reveal N_w(min),the minimum number required for the loop to exhibit realistic (fully hydrated) behavior.We have also studied protein surface coverage,as well as diffusion and residence times for water molecules as a function of N_w.A number of other modeling parameters are also tested.These include the number of environmental protein atoms explicitly considered in the model as well as two ways to constrain the water molecules to the vicinity of the loop (where we find one of these methods to perform better when N_w is small).The results (for the root-mean-square deviation and its fluctuations for four loops) are further compared to much larger,fully solvated systems (using approx 10 000 water molecules under periodic boundary conditions and Ewald electrostatics) and to results for the generalized Born surface area (GBSA) implicit solvation model.We find that the loop backbone can stabilize with a surprisingly small number of water molecules (as low as five molecules per amino acid residue).The side chains of the loop require a somewhat larger N_w,where the atomic fluctuations become too small if N_w is further reduced.Thus,in general,we find adequate hydration to occur at roughly 12 water molecules per residue.This is an important result because,at this hydration level,computational times are comparable to those required for GBSA.Therefore,these "minimalist explicit models"can provide a viable and potentially more accurate alternative.The importance of protein loop modeling is discussed in the context of these,and other,loop models,along with other challenges including the relevance of an appropriate free-energy simulation methodology for the assessment of conformational stability.
展开▼
