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Polar Contribution (polar + contribution)
Selected AbstractsConverging free energy estimates: MM-PB(GB)SA studies on the protein,protein complex Ras,RafJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 2 2004Holger Gohlke Abstract Estimating protein,protein interaction energies is a very challenging task for current simulation protocols. Here, absolute binding free energies are reported for the complex H-Ras/C-Raf1 using the MM-PB(GB)SA approach, testing the internal consistency and model dependence of the results. Averaging gas-phase energies (MM), solvation free energies as determined by Generalized Born models (GB/SA), and entropic contributions calculated by normal mode analysis for snapshots obtained from 10 ns explicit-solvent molecular dynamics in general results in an overestimation of the binding affinity when a solvent-accessible surface area-dependent model is used to estimate the nonpolar solvation contribution. Applying the sum of a cavity solvation free energy and explicitly modeled solute,solvent van der Waals interaction energies instead provides less negative estimates for the nonpolar solvation contribution. When the polar contribution to the solvation free energy is determined by solving the Poisson,Boltzmann equation (PB) instead, the calculated binding affinity strongly depends on the atomic radii set chosen. For three GB models investigated, different absolute deviations from PB energies were found for the unbound proteins and the complex. As an alternative to normal-mode calculations, quasiharmonic analyses have been performed to estimate entropic contributions due to changes of solute flexibility upon binding. However, such entropy estimates do not converge after 10 ns of simulation time, indicating that sampling issues may limit the applicability of this approach. Finally, binding free energies estimated from snapshots of the unbound proteins extracted from the complex trajectory result in an underestimate of binding affinity. This points to the need to exercise caution in applying the computationally cheaper "one-trajectory-alternative" to systems where there may be significant changes in flexibility and structure due to binding. The best estimate for the binding free energy of Ras,Raf obtained in this study of ,8.3 kcal mol,1 is in good agreement with the experimental result of ,9.6 kcal mol,1, however, further probing the transferability of the applied protocol that led to this result is necessary. © 2003 Wiley Periodicals, Inc. J Comput Chem 2: 238,250, 2003 [source] Application of hydrophilic interaction chromatography retention coefficients for predicting peptide elution with TFA and methanesulfonic acid ion-pairing reagentsJOURNAL OF SEPARATION SCIENCE, JSS, Issue 6-7 2010Chad E. Wujcik Abstract Hydrophilic retention coefficients for 17 peptides were calculated based on retention coefficients previously published for TSKgel silica-60 and were compared with the experimental elution profile on a Waters Atlantis HILIC silica column using TFA and methanesulfonic acid (MSA) as ion-pairing reagents. Relative peptide retention could be accurately determined with both counter-ions. Peptide retention and chromatographic behavior were influenced by the percent acid modifier used with increases in both retention and peak symmetry observed at increasing modifier concentrations. The enhancement of net peptide polarity through MSA pairing shifted retention out by nearly five-fold for the earliest eluting peptide, compared with TFA. Despite improvements in retention and efficiency (Neff) for MSA over TFA, a consistent reduction in calculated selectivity (,) was observed. This result is believed to be attributed to the stronger polar contribution of MSA masking and diminishing the underlying influence of the amino acid residues of each associated peptide. Finally, post-column infusion of propionic acid and acetic acid was evaluated for their potential to recover signal intensity for TFA and MSA counter-ions for LC-ESI-MS applications. Acetic acid generally yielded more substantial signal improvements over propionic acid on the TFA system while minimal benefits and some further reductions were noted with MSA. [source] Polymer Chain Collapse in Supercritical Fluids.MACROMOLECULAR SYMPOSIA, Issue 1 2009Abstract The phase behavior of a polymer in a supercritical solvent at the LCST equilibrium limits is described in this work, in the proximity of , point, proposing the use of a conformational parameter, ,. The results obtained by molecular simulation in an NVT ensemble have been correlated by extensive, varied experimental information. The relationship between polymer/solvent solubility parameters has shown that the behavior of these systems is a function of the energetic structure-interaction relationship between the polymer chain and the solvent. , results in a generalized parameter indicative of the phase stability of the solution. At greater magnitudes, the solution becomes unstable, requiring elevated pressure to stabilize. However, stable solutions are found at lower pressures when , approaches 1. The experimental evidence, together with the determination of the solubility parameter with the Sanchez-Lacombe equation (also obtained from the literature) strengthens this observation. The analysis of the polar contribution on the Hansen Parameter (HSP) enables their effect to be studied in systems where high polar interactions between the polymer and solvent (as in the case of biopolymers) are expected. [source] Surface characterization and study of Langmuir films of poly(4-vinylpyridine) quaternized with n -alkylbromidePOLYMER INTERNATIONAL, Issue 8 2001Ligia Gargallo Abstract The surface behaviour of poly(4-vinylpyridine)s (P4VP) quaternized with four different alkyl chains (pentyl, hexyl, octyl and decy bromide) were studied. Surface pressure,area isotherms (,,A) at the air,water interface were determined. Depending on the length of the side-chains, the ,,A isotherms show a plateau region. An extensive plateau is observed for n,>,6. The plateau pressures are similar for n,,=,8 and n,,=,10. The monolayers are stable and exhibit hysteresis phenomena. Brewster angle microscopy (BAM) is used to monitor the monolayer topography of the polymer on water subphase. To obtain information about the surface energy (SE) and the degree of hydrophobicity of these systems, we have estimated the critical surface tension, ,c, and the dispersion force and polar contributions to SE, ,D and ,P, respectively, by measurements of the contact angle (CA) of water and bromobenzene on the polymer surface. The results obtained are depend on the length of the alkyl lateral chain of the functionalized polymers. © 2001 Society of Chemical Industry [source] Chaperone-like activities of different molecular forms of ,-casein.BIOPOLYMERS, Issue 8 2009Importance of polarity of N-terminal hydrophilic domain Abstract As a member of intrinsically unstructured protein family, ,-casein (,-CN) contains relatively high amount of prolyl residues, adopts noncompact and flexible structure and exhibits chaperone-like activity in vitro. Like many chaperones, native ,-CN does not contain cysteinyl residues and exhibits strong tendencies for self-association. The chaperone-like activities of three recombinant ,-CNs wild type (WT) ,-CN, C4 ,-CN (with cysteinyl residue in position 4) and C208 ,-CN (with cysteinyl residue in position 208), expressed and purified from E. coli, which, consequently, lack the phosphorylated residues, were examined and compared with that of native ,-CN using insulin and alcohol dehydrogenase as target/substrate proteins. The dimers (,-CND) of C4-,-CN and C208 ,-CN were also studied and their chaperone-like activities were compared with those of their monomeric forms. Lacking phosphorylation, WT ,-CN, C208 ,-CN, C4 ,-CN and C4 ,-CND exhibited significantly lower chaperone-like activities than native ,-CN. Dimerization of C208 ,-CN with two distal hydrophilic domains considerably improved its chaperone-like activity in comparison with its monomeric form. The obtained results demonstrate the significant role played by the polar contributions of phosphorylated residues and N-terminal hydrophilic domain as important functional elements in enhancing the chaperone-like activity of native ,-CN. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 623,632, 2009. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] | |||||||||||||