Shayantani Mukherjee, Sean M. Law, Michael Feig
Biophysical Journal (2009) 96, 1707-1720
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Postreplication DNA mismatch repair is essential for maintaining the integrity of genomic information in prokaryotes and eukaryotes. The first step in mismatch repair is the recognition of base-base mismatches and insertions/deletions by bacterial MutS or eukaryotic MSH2-MSH6. Crystal structures of both proteins bound to mismatch DNA reveal a similar molecular architecture but provide limited insight into the detailed molecular mechanism of long-range allostery involved in mismatch recognition and repair initiation. This study describes normal-mode calculations of MutS and MSH2-MSH6 with and without DNA. The results reveal similar protein flexibilities and suggest common dynamic and functional characteristics. A strongly correlated motion is present between the lever domain and ATPase domains, which suggests a pathway for long-range allostery from the N-terminal DNA binding domain to the C-terminal ATPase domains, as indicated by experimental studies. A detailed analysis of individual low-frequency modes of both MutS and MSH2-MSH6 shows changes in the DNA-binding domains coupled to the ATPase sites, which are interpreted in the context of experimental data to arrive at a complete molecular-level mismatch recognition cycle. Distinct conformational states are proposed for DNA scanning, mismatch recognition, repair initiation, and sliding along DNA after mismatch recognition. Hypotheses based on the results presented here form the basis for further experimental and computational studies.

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Michael Feig
Journal of Chemical Theory and Computation (2008) in press
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The conformational preference for different φ/ψ backbone torsion angles is a key determinant of peptide and protein secondary structure. Often, dipeptides are used as models for understanding protein backbone dynamics and to derive force field parameters. Here, the question is examined to what extent the conformational preferences in dipeptides reflect the backbone dynamics in polypeptides and proteins and to what extent an alanine dipeptide-based backbone torsion parametrization can lead to accurate reproduction of amino acid dependent φ/ψ preferences in protein structures. Results from a comparison of the analysis of Protein Data Bank (PDB) structures with long simulations of selected proteins and amino acid dipeptides suggest that a common alanine dipeptide-based torsion potential does in fact lead to excellent agreement between protein simulations and PDB structures. At the same time, the φ/ψ preferences in the dipeptides are significantly different, suggesting that dipeptides are not good model systems for studying protein backbone dynamics.

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Seiichiro Tanizaki, Jacob W. Clifford, Brian D. Connelly, Michael Feig
Biophysical Journal (2008) 94 747-759
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Biological systems provide a complex environment that can be understood in terms of its dielectric properties. High concentrations of macromolecules and cosolvents effectively reduce the dielectric constant of cellular environments, thereby affecting the conformational sampling of biomolecules. To examine this effect in more detail, the conformational preference of alanine dipeptide, poly-alanine, and melittin in different dielectric environments is studied with computer simulations based on recently developed generalized Born methodology. Results from these simulations suggest that extended conformations are favored over α-helical conformations at the dipeptide level at and below dielectric constants of 5-10. Furthermore, lower-dielectric environments begin to significantly stabilize helical structures in poly-alanine at ε = 20. In the more complex peptide melittin, different dielectric environments shift the equilibrium between two main conformations: a nearly fully extended helix that is most stable in low dielectrics and a compact, V-shaped conformation consisting of two helices that is preferred in higher dielectric environments. An additional conformation is only found to be significantly populated at intermediate dielectric constants. Good agreement with previous studies of different peptides in specific, less-polar solvent environments, suggest that helix stabilization and shifts in conformational preferences in such environments are primarily due to a reduced dielectric environment rather than specific molecular details. The findings presented here make predictions of how peptide sampling may be altered in dense cellular environments with reduced dielectric response.

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Andrew Stumpff-Kane, Katarzyna Maksimiak, Michael S. Lee, Michael Feig
Proteins (2007) 70 1345-1356
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Protein structure refinement from comparative models with the goal of predicting structures at near-experimental accuracy remains an unsolved problem. Structure refinement might be achieved with an iterative protocol where the most native-like structure from a set of decoys generated from an initial model in one cycle is used as the starting structure for the next cycle. Conformational sampling based on the coarse-grained SICHO model, atomic level of detail molecular dynamics simulations, and normal-mode analysis is compared in the context of such a protocol. All of the sampling methods can achieve significant refinement close to experimental structures, although the distribution of structures and the ability to reach native-like structures differs greatly. Implications for the practical application of such sampling methods and the requirements for scoring functions in an iterative refinement protocol are analyzed in the context of theoretical predictions for the distribution of protein-like conformations with a random sampling protocol.

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