The ability of proteins to locate specific sites or structures among a vast excess of nonspecific DNA is a fundamental theme in biology. Yet the basic principles that govern these mechanisms remain poorly understood. For example, mismatch repair proteins must scan millions of base pairs to find rare biosynthetic errors, and they then must probe the surrounding region to identify the strand discrimination signals necessary to distinguish the parental and daughter strands. To determine how these proteins might function we used single-molecule optical microscopy to answer the following question: how does the mismatch repair complex Msh2-Msh6 interrogate undamaged DNA? Here we show that Msh2-Msh6 slides along DNA via one-dimensional diffusion. These findings indicate that interactions between Msh2-Msh6 and DNA are dominated by lateral movement of the protein along the helical axis and have implications for how MutS family members travel along DNA at different stages of the repair reaction.

Protein G is folded with an all-atom Monte Carlo simulation by using a Gō potential. When folding is monitored by using burial of the lone tryptophan in protein G as the reaction coordinate, the ensemble kinetics is single exponential. Other experimental observations, such as the burst phase and mutational data, are also reproduced. However, more detailed analysis reveals that folding occurs over three distinct, three-state pathways. We show that, because of this tryptophan's asymmetric location in the tertiary fold, its burial (i) does not detect certain intermediates and (ii) may not correspond to the folding event. This finding demonstrates that ensemble averaging can disguise the presence of multiple pathways and intermediates when a non-ideal reaction coordinate is used. Finally, all observed folding pathways eventually converge to a common rate-limiting step, which is the formation of a specific nucleus involving hydrophobic core residues. These residues are conserved in the ubiquitin superfamily and in a phage display experiment, suggesting that fold topology is a strong determinant of the transition state.B alancing realism and computational tractability has been the central issue when simulating protein folding on the computer. Recently, an impressive parallelization effort led to a 1-s full-scale molecular dynamics (MD) trajectory of the 36-residue villin headpiece (1). Unfortunately, the use of such simulations to rigorously study folding is still several years away because single domain proteins fold on timescales that are at least two orders of magnitude longer (2). Moreover, because folding is a stochastic process, averaging over multiple runs is required. These computational problems can be partly alleviated by investigating folding kinetics indirectly by using the construction of free energy landscapes (3) or unfolding at high temperatures (4).Recently, two complementary approaches have directly accessed the timescales relevant to folding. The first makes use of ensemble dynamics (5), whereby the long waiting times associated with rare events-which plague any simulation being run serially in time-are eliminated by running parallel simulations and allowing them to exchange states whenever a barrier crossing occurs. The second approach extends existing off-lattice coarsegrained Monte Carlo (MC) simulations (6) by introducing all-atom structural realism. Computational costs are minimized by (i) moving only backbone and sidechain torsional degrees of freedom (which are the ''softest'' modes in a polymer) and (ii) by using coarse-grained potentials. This simulation has been used with the Gō (7) and sequence-based potentials (8) to fold helices, hairpins, crambin, and protein A.In this paper, we present ensemble kinetic data of the wellcharacterized 57-residue protein G (9) (Fig. 1A) by using this all-atom MC technique with a Gō potential. Under this potential, only interactions present in the native conformation are attractive. Although the native state is the global energy minimum by construction, no...

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