Beta‐hairpin restraint potentials for calculations of potentials of mean force as a function of beta‐hairpin tilt,rotation, and distance

We have developed a set of restraint potentials for β‐hairpin tilt relative to the membrane normal, β‐hairpin rotation around the β‐hairpin axis, and hairpin–hairpin distance. Such restraint potentials enable us to characterize the molecular basis of specific β‐hairpin tilt and rotation in membranes and hairpin–hairpin interactions at the atomic level by sampling their conformational space along these degrees of freedom, i.e., reaction coordinates, during molecular dynamics simulations. We illustrate the efficacy of the β‐hairpin restraint potentials by calculating the potentials of mean force (PMFs) as a function of tilt and rotation angles of protegrin‐1 (PG‐1), a β‐hairpin antimicrobial peptide, in an implicit membrane model. The peptide association in the membrane is also examined by calculating the PMFs as a function of distance between two PG‐1 peptides in various dimer interfaces. These novel restraint potentials are found to perform well in each of these cases and are expected to be a useful means to study the microscopic driving forces of insertion, tilting, and rotation of β‐hairpin peptides in membranes as well as their association in aqueous solvent or membrane environments particularly when combined with explicit solvent models. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009     

Site‐directed analysis on protein hydrophobicity

Hydrophobicity of a protein is considered to be one of the major intrinsic factors dictating the protein aggregation propensity. Understanding how protein hydrophobicity is determined is, therefore, of central importance in preventing protein aggregation diseases and in the biotechnological production of human therapeutics. Traditionally, protein hydrophobicity is estimated based on hydrophobicity scales determined for individual free amino acids, assuming that those scales are unaltered when amino acids are embedded in a protein. Here, we investigate how the hydrophobicity of constituent amino acid residues depends on the protein context. To this end, we analyze the hydration free energy—free energy change on hydration quantifying the hydrophobicity—of the wild‐type and 21 mutants of amyloid‐beta protein associated with Alzheimer's disease by performing molecular dynamics simulations and integral‐equation calculations. From detailed analysis of mutation effects on the protein hydrophobicity, we elucidate how the protein global factor such as the total charge as well as underlying protein conformations influence the hydrophobicity of amino acid residues. Our results provide a unique insight into the protein hydrophobicity for rationalizing and predicting the protein aggregation propensity on mutation, and open a new avenue to design aggregation‐resistant proteins as biotherapeutics. © 2014 Wiley Periodicals, Inc.     

Editorial

Abstract

Asymmetric syntheses of optically active polymethacrylate, polyacrylate, polyacrylamide, and polyisocyanate with helical conformation and their chiral recognition abilities are described. 1-Phenyldibenzosuberyl methacrylate (PDBSMA) gave a purely onehanded-helical, optically active polymer ([α]₃₆₅ +1670 ～ +1780º) with almost perfectly isotactic structure by anionic polymerization using optically active initiators. Radical polymerizations of PDBSMA using chiral initiators, chain transfer agents, and additives also afforded optically active polymers with a prevailing onehanded helicity. Triphenylmethyl acrylate yielded an optically active, helical polymer ([α]₃₆₅ +102º) having a dyad isotacticity of 70% using an optically active anionic initiator. Although the polyacrylate demonstrated chiral recognition ability as a chiral stationary phase for HPLC, the ability was low mainly because of the low degree of one-handedness. N-(3-Chlorophenyl)-N-phenylacrylamide gave an optically active, helical polymer ([α]_365–343º) in the asymmetric anionic polymerization; the polymer had a dyad tacticity of 77%. Optically active polyisocyanates with a predominantly one-handed helical conformation were prepared in homo-and co-polymerization of optically active phenyl isocyanate derivative. These polyisocyanates showed the ability to discriminate enantiomers in solution.