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Delineating structures of the transition states in protein folding reactions has provided great insight into the mechanisms by which proteins fold. The most common method for obtaining this information is Φ‐value analysis, which is carried out by measuring the changes in the folding and...
Muscular dystrophy (MD) is the most common genetic lethal disorder in children. Mutations in dystrophin trigger the most common form of MD, Duchenne, and its allelic variant Becker MD. Utrophin is the closest homologue and has been shown to compensate for the loss of dystrophin in human disease...
Silencing in RNAi is strongly affected by guide‐strand/target‐mRNA mismatches. Target nucleation is thought to occur at positions 2–8 of the guide (“seed region”); successful hybridization in this region is the primary determinant of target‐binding affinity and hence target cleavage....
We employ all‐atom structure‐based models with a force field with multiple energetic basins for the C‐terminal (residues 166–226) of the mammalian prion protein. One basin represents the known alpha‐helical (αH) structure while the other represents the same residues in a left‐handed...
It is crucial to consider dynamics for understanding the biological function of proteins. We used a large number of molecular dynamics (MD) trajectories of nonhomologous proteins as references and examined static structural features of proteins that are most relevant to fluctuations. We examined...
Archaeal Initiation Factor 2 is a GTPase involved in protein biosynthesis. In its GTP‐bound, “ON” conformation, it binds an initiator tRNA and carries it to the ribosome. In its GDP‐bound, “OFF” conformation, it dissociates from tRNA. To understand the specific binding of GTP and GDP...
α‐Synuclein is the principal component of the Lewy body deposits that are characteristic of Parkinson's disease. In vivo, and under physiological conditions in vitro, α‐synuclein aggregates to form amyloid fibrils, a process that is likely to be associated with the development of...
The hexapeptide Ser‐Gly‐Ala‐Gly‐Lys‐Thr has been synthesized and characterized. It was designed as a minimal soluble peptide that would be likely to have the phosphate‐binding properties observed in the P‐loops of proteins that bind the β‐phosphate of GTP or ATP. The...
Molecular dynamics simulations of a keratin/peptide complex have been conducted to predict the binding affinity of four different peptides toward human hair. Free energy calculations on the peptides' interaction with the keratin model demonstrated that electrostatic interactions are believed to...
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