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Continuum Solvation Model (continuum + solvation_model)
Selected AbstractsABSINTH: A new continuum solvation model for simulations of polypeptides in aqueous solutionsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 5 2009Andreas Vitalis Abstract A new implicit solvation model for use in Monte Carlo simulations of polypeptides is introduced. The model is termed ABSINTH for self- Assembly of Biomolecules Studied by an Implicit, Novel, and Tunable Hamiltonian. It is designed primarily for simulating conformational equilibria and oligomerization reactions of intrinsically disordered proteins in aqueous solutions. The paradigm for ABSINTH is conceptually similar to the EEF1 model of Lazaridis and Karplus (Proteins 1999, 35, 133). In ABSINTH, the transfer of a polypeptide solute from the gas phase into a continuum solvent is the sum of a direct mean field interaction (DMFI), and a term to model the screening of polar interactions. Polypeptide solutes are decomposed into a set of distinct solvation groups. The DMFI is a sum of contributions from each of the solvation groups, which are analogs of model compounds. Continuum-mediated screening of electrostatic interactions is achieved using a framework similar to the one used for the DMFI. Promising results are shown for a set of test cases. These include the calculation of NMR coupling constants for short peptides, the assessment of the thermal stability of two small proteins, reversible folding of both an ,-helix and a ,-hairpin forming peptide, and the polymeric properties of intrinsically disordered polyglutamine peptides of varying lengths. The tests reveal that the computational expense for simulations with the ABSINTH implicit solvation model increase by a factor that is in the range of 2.5,5.0 with respect to gas-phase calculations. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009 [source] Computational alanine scanning of the 1:1 human growth hormone,receptor complexJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 1 2002Shuanghong Huo Abstract The MM-PBSA (Molecular Mechanics,Poisson,Boltzmann surface area) method was applied to the human Growth Hormone (hGH) complexed with its receptor to assess both the validity and the limitations of the computational alanine scanning approach. A 400-ps dynamical trajectory of the fully solvated complex was simulated at 300 K in a 101 Å×81 Å×107 Å water box using periodic boundary conditions. Long-range electrostatic interactions were treated with the particle mesh Ewald (PME) summation method. Equally spaced snapshots along the trajectory were chosen to compute the binding free energy using a continuum solvation model to calculate the electrostatic desolvation free energy and a solvent-accessible surface area approach to treat the nonpolar solvation free energy. Computational alanine scanning was performed on the same set of snapshots by mutating the residues in the structural epitope of the hormone and the receptor to alanine and recomputing the ,Gbinding. To further investigate a particular structure, a 200-ps dynamical trajectory of an R43A hormone,receptor complex was simulated. By postprocessing a single trajectory of the wild-type complex, the average unsigned error of our calculated ,,Gbinding is ,1 kcal/mol for the alanine mutations of hydrophobic residues and polar/charged residues without buried salt bridges. When residues involved in buried salt bridges are mutated to alanine, it is demonstrated that a separate trajectory of the alanine mutant complex can lead to reasonable agreement with experimental results. Our approach can be extended to rapid screening of a variety of possible modifications to binding sites. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 15,27, 2002 [source] Spectroscopy and Photoreactivity of Trichochromes: Molecular Components of Pheomelanins,PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 1 2006John D. Simon ABSTRACT The trichochromes are a class of small molecules present in pheomelanin (the red melanin) and absent in eumelanin (the black melanin). Herein trichochrome F (TF) and decarboxy-trichochrome C (dTC) are examined. Both trichochromes are characterized by a visible absorption band, which is shown to be the result of overlapping transitions of the cis and trans isomers. The temperature dependence of the absorption spectrum of dTC suggests the additional presence of equilibrium between the enol and keto forms of the molecule. These conclusions are supported by ground-state energies of these isomers obtained using a continuum solvation model. Near-infrared emission measurements were not able to detect photoproduction of 1O2, and spin-trapping experiments revealed formation of O2*- . DNA nicking assays also revealed a low level of light-induced aerobic activity of dTC, suggesting a quantum efficiency of at most 5 × 10 -6 for the photo-generation of O2*- . These results are consistent with pump-probe optical experiments, which reveal efficient and nearly complete ground-state recovery within a few picoseconds of excitation. Both trichochromes are efficient quenchers of 1O2, exhibiting a bimolecular rate constant comparable with vitamin C. These results suggest that trichochromes could serve a protective role in pheomelanin pigments. [source] Intermolecular interaction studies of winter flounder antifreeze protein reveal the existence of thermally accessible binding stateBIOPOLYMERS, Issue 2 2004Dat H. Nguyen Abstract The physical nature underlying intermolecular interactions between two rod-like winter flounder antifreeze protein (AFP) molecules and their implication for the mechanism of antifreeze function are examined in this work using molecular dynamics simulations, augmented with free energy calculations employing a continuum solvation model. The energetics for different modes of interactions of two AFP molecules is examined in both vacuum and aqueous phases along with the water distribution in the region encapsulated by two antiparallel AFP backbones. The results show that in a vacuum two AFP molecules intrinsically attract each other in the antiparallel fashion, where their complementary charge side chains face each other directly. In the aqueous environment, this attraction is counteracted by both screening and entropic effects. Therefore, two nearly energetically degenerate states, an aggregated state and a dissociated state, result as a new aspect of intermolecular interaction in the paradigm for the mechanism of action of AFP. The relevance of these findings to the mechanism of function of freezing inhibition in the context of our work on Antarctic cod antifreeze glycoprotein (Nguyen et al., Biophysical Journal, 2002, Vol. 82, pp. 2892,2905) is discussed. © 2004 Wiley Periodicals, Inc. Biopolymers, 2004 [source] Computational Investigations on the General Reaction Profile and Diastereoselectivity in Sulfur Ylide Promoted AziridinationCHEMISTRY - A EUROPEAN JOURNAL, Issue 17 2007Deepa Janardanan Abstract Mechanism and diastereoselectivity of sulfur ylide promoted aziridination reactions were studied by density functional theory with inclusion of solvent effects through the continuum solvation model. The general reaction pathway was modeled for the addition of substituted sulfur ylides (Me2S+CH,R) to an aldimine ((E)-methyl ethylidenecarbamate, MeHCNCO2Me). The nature of the substituents on the ylidic carbon atom substantially affects the reaction profile. The stabilized (R=COMe) and semistabilized (R=Ph) ylides follow a cisoid addition mode leading to trans aziridines via anti betaine intermediates. The simplest model ylide (unstabilized, R=H) underwent cisoid addition in a similar fashion. In the case of stabilized ylides product diastereoselectivity is controlled by the barriers of the elimination step leading to the 2,3- trans aziridine, whereas it is decided in the addition step in the case of semistabilized ylides. The importance of steric and electronic factors in diastereoselective addition (2 and 5) and elimination (5) transition states was established. Comparison of results obtained with the gas-phase optimized geometries and with the fully optimized solvent-phase geometries reveals that the inclusion of solvent effects does not bring about any dramatic changes in the reaction profiles for all three kinds of ylides. In particular, diastereoselectivity for both kinds of ylides was found to be nearly the same in both these approaches. [source] | ||||||||||