Refolding molecular dynamics simulations of small- and middle-sized proteins in an explicit solvent

Probing the protein-folding mechanism using denaturant and temperature effects on rate constants

Protein folding has been extensively studied, but many questions remain regarding the mechanism. Characterizing early unstable intermediates and the high-free-energy transition state (TS) will help answer some of these. Here, we use effects of denaturants (urea, guanidinium chloride) and temperature on folding and unfolding rate constants and the overall equilibrium constant as probes of surface area changes in protein folding. We interpret denaturant kinetic m-values and activation heat capacity changes for 13 proteins to determine amounts of hydrocarbon and amide surface buried in folding to and from TS, and for complete folding. Predicted accessible surface area changes for complete folding agree in most cases with structurally determined values. We find that TS is advanced (50-90% of overall surface burial) and that the surface buried is disproportionately amide, demonstrating extensive formation of secondary structure in early intermediates. Models of possible pre-TS intermediates with all elements of the native secondary structure, created for several of these proteins, bury less amide and hydrocarbon surface than predicted for TS. Therefore, we propose that TS generally has both the native secondary structure and sufficient organization of other regions of the backbone to nucleate subsequent (post-TS) formation of tertiary interactions. The approach developed here provides proof of concept for the use of denaturants and other solutes as probes of amount and composition of the surface buried in coupled folding and other large conformational changes in TS and intermediates in protein processes.

Stabilization of the spectrin-like domains of nesprin-1α by the evolutionarily conserved "adaptive" domain

Nesprins are located at the outer and inner membranes of the nuclear envelope and help link the cytoskeleton to the nucleoskeleton. Nesprin-1α, located at the inner nuclear membrane, binds to A-type lamins and emerin and has homology to spectrin-repeat proteins. However, the mechanical and thermodynamic properties of the spectrin-like repeats (SLRs) of nesprin-1α and the potential structural contributions of the unique central domain were untested. In other spectrin superfamily proteins, tandem spectrin-repeat domains undergo cooperatively coupled folding and unfolding. We hypothesized that the large central domain, which interrupts SLRs and is conserved in other nesprin isoforms, might confer unique structural properties. To test this model we measured the thermal unfolding of nesprin-1α fragments using circular dichroism and dynamic light scattering. The SLRs in nesprin-1α were found to have structural and thermodynamic properties typical of spectrins. The central domain had relatively little secondary structure as an isolated fragment, but significantly stabilized larger SLR-containing molecules by increasing their overall helicity, thermal stability and cooperativity of folding. We suggest this domain, now termed the 'adaptive' domain (AD), also strengthens dimerization and inhibits unfolding. Further engineering of the isolated AD, and AD-containing nesprin molecules, may yield new information about the higher-order association of cooperative protein motifs.

Large-scale molecular-dynamics simulation of nanoscale hydrophobic interaction and nanobubble formation

We performed large-scale molecular-dynamics simulation of nanoscale hydrophobic interaction manifested by the formation of nanobubble between nanometer-sized hydrophobic clusters at constrained equilibrium. Particular attention is placed on the tendency of formation and stability of nanobubbles in between model nanoassemblies which are composed of hydrophobic clusters (or patches) embedded in a hydrophilic substrate. On the basis of physical behavior of nanobubble formation, we observed a change from short-range molecular hydrophobic interaction to midrange nanoscopic interaction when the length scale of hydrophobe approaches to about 1 nm. We investigated the behavior of nanobubble formation with several different patterns of nonpolar-site distribution on the nanoassemblies but always keeping a constant ratio of nonpolar to polar monomer sites. Dynamical properties of confined water molecules in between nanoassemblies are also calculated.

Free energy surfaces of miniproteins with a ββα motif: Replica exchange molecular dynamics simulation with an implicit solvation model

Designed miniproteins with a betabetaalpha motif, such as BBA5, 1FSD, and 1PSV can serve as a benchmark set to test the validity of all-atom force fields with computer simulation, because they contain all the basic structural elements in protein folding. Unfortunately, it was found that the standard all-atom force fields with the generalized Born (GB) implicit solvation model tend to produce distorted free energy surfaces for the betabetaalpha proteins, not only because energetically those proteins need to be described by more balanced weights of the alpha- and beta-strands, but also because the GB implicit solvation model suffers from overestimated salt bridge effects. In an attempt to resolve these problems, we have modified one of the standard all-atom force fields in conjunction with the GB model, such that each native state of the betabetaalpha proteins is in its free energy minimum state with reasonable energy barriers separating local minima. With this modified energy model, the free energy contour map in each protein was constructed from the replica exchange molecular dynamics REMD simulation. The resulting free energy surfaces are significantly improved in comparison with previous simulation results and consistent with general views on small protein folding behaviors with realistic topology and energetics of all three proteins.