Kooperativer Bibliotheksverbund

Berlin Brandenburg

and
and

Your email was sent successfully. Check your inbox.

An error occurred while sending the email. Please try again.

Proceed reservation?

Export
Filter
Type of Medium
Language
Year
  • 1
    Language: English
    In: Journal of the American Chemical Society, 20 June 2012, Vol.134(24), pp.10039-46
    Description: The specific binding sites of Hofmeister ions with an uncharged 600-residue elastin-like polypeptide, (VPGVG)(120), were elucidated using a combination of NMR and thermodynamic measurements along with molecular dynamics simulations. It was found that the large soft anions such as SCN(-) and I(-) interact with the polypeptide backbone via a hybrid binding site that consists of the amide nitrogen and the adjacent α-carbon. The hydrocarbon groups at these sites bear a slight positive charge, which enhances anion binding without disrupting specific hydrogen bonds to water molecules. The hydrophobic side chains do not contribute significantly to anion binding or the corresponding salting-in behavior of the biopolymer. Cl(-) binds far more weakly to the amide nitrogen/α-carbon binding site, while SO(4)(2-) is repelled from both the backbone and hydrophobic side chains of the polypeptide. The Na(+) counterions are also repelled from the polypeptide. The identification of these molecular-level binding sites provides new insights into the mechanism of peptide-anion interactions.
    Keywords: Ions -- Chemistry ; Peptides -- Chemistry
    ISSN: 00027863
    E-ISSN: 1520-5126
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 2
    Language: English
    In: The journal of physical chemistry. B, 18 September 2014, Vol.118(37), pp.10979-88
    Description: Cosolvent effects on protein or polymer collapse transitions are typically discussed in terms of a two-state free energy change that is strictly linear in cosolute concentration. Here we investigate in detail the nonlinear thermodynamic changes of the collapse transition occurring at the lower critical solution temperature (LCST) of the role-model polymer poly(N-isopropylacrylamide) [PNIPAM] induced by Hofmeister salts. First, we establish an equation, based on the second-order expansion of the two-state free energy in concentration and temperature space, which excellently fits the experimental LCST curves and enables us to directly extract the corresponding thermodynamic parameters. Linear free energy changes, grounded on generic excluded-volume mechanisms, are indeed found for strongly hydrated kosmotropes. In contrast, for weakly hydrated chaotropes, we find significant nonlinear changes related to higher order thermodynamic derivatives of the preferential interaction parameter between salts and polymer. The observed non-monotonic behavior of the LCST can then be understood from a not yet recognized sign change of the preferential interaction parameter with salt concentration. Finally, we find that solute partitioning models can possibly predict the linear free energy changes for the kosmotropes, but fail for chaotropes. Our findings cast strong doubt on their general applicability to protein unfolding transitions induced by chaotropes.
    Keywords: Polymers -- Chemistry
    ISSN: 15206106
    E-ISSN: 1520-5207
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 3
    Language: English
    In: Journal of Physical Chemistry B, Sept 18, 2014, Vol.118(37), pp.10979-10988
    Keywords: Thermodynamics – Analysis ; Hofmeister Effects – Analysis
    ISSN: 1520-6106
    Source: Cengage Learning, Inc.
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 4
    Language: English
    In: Journal of Physical Chemistry A, Oct 20, 2011, Vol.115(41), p.11193-11201
    Keywords: Arginine -- Structure ; Arginine -- Chemical Properties ; Guanidines -- Chemical Properties ; Guanidines -- Structure ; Molecular Dynamics -- Usage ; Peptide Bonds -- Analysis ; Protein Structure -- Research
    ISSN: 1089-5639
    Source: Cengage Learning, Inc.
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 5
    Language: English
    In: The Journal of Chemical Physics, 14 August 2015, Vol.143(6)
    Description: We introduce a set of charged patchy particle models (CPPMs) in order to systematically study the influence of electrostatic charge patchiness and multipolarity on macromolecular interactions by means of implicit-solvent, explicit-ion Langevin dynamics simulations employing the Gromacs software. We consider well-defined zero-, one-, and two-patched spherical globules each of the same net charge and (nanometer) size which are composed of discrete atoms. The studied mono- and multipole moments of the CPPMs are comparable to those of globular proteins with similar size. We first characterize ion distributions and electrostatic potentials around a single CPPM. Although angle-resolved radial distribution functions reveal the expected local accumulation and depletion of counter- and co-ions around the patches, respectively, the orientation-averaged electrostatic potential shows only a small variation among the various CPPMs due to space charge cancellations. Furthermore, we study the orientation-averaged potential of mean force (PMF), the number of accumulated ions on the patches, as well as the CPPM orientations along the center-to-center distance of a pair of CPPMs. We compare the PMFs to the classical Derjaguin-Verwey-Landau-Overbeek theory and previously introduced orientation-averaged Debye-Hückel pair potentials including dipolar interactions. Our simulations confirm the adequacy of the theories in their respective regimes of validity, while low salt concentrations and large multipolar interactions remain a challenge for tractable theoretical descriptions.
    Keywords: Articles
    ISSN: 0021-9606
    E-ISSN: 1089-7690
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 6
    Language: English
    In: The journal of physical chemistry. A, 26 November 2012, Vol.116(46), pp.11199-210
    Description: We study the vibrational decoherence dynamics of an iodine molecule in a finite krypton cluster comprising the first solvation shell. A normal mode analysis allows us to successively increase the complexity of the description. For the ground state dynamics, comparison with experimental matrix results shows that already four degrees of freedom are sufficient to capture the main decoherence mechanism. For electronically excited iodine, we model the vibrational dynamics of initial Schrödinger cat-like states by the semiclassical hybrid dynamics [Grossmann, F. J. Chem. Phys. 2006, 125, 014111] and full quantum calculations, where available. Good agreement of the results is found for a reduced model with three degrees of freedom. We find non-Gaussian distortions of the bath density matrix, which is a necessary condition, if Schrödinger catlike states in the bath are to be identified. However, in contrast to the experiment [Segale, D.; et al. J. Chem. Phys. 2005, 122, 111104], we observe only incoherent superpositions of bath vibrational states.
    Keywords: Chemistry;
    ISSN: 10895639
    E-ISSN: 1520-5215
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 7
    Language: English
    In: The journal of physical chemistry. B, 21 July 2011, Vol.115(28), pp.8910-24
    Description: Using a combination of experimental techniques (circular dichroism, differential scanning calorimetry, and NMR) and molecular dynamics simulations, we performed an extensive study of denaturation of the Trp-cage miniprotein by urea and guanidinium. The experiments, despite their different sensitivities to various aspects of the denaturation process, consistently point to simple, two-state unfolding process. Microsecond molecular dynamics simulations with a femtosecond time resolution allow us to unravel the detailed molecular mechanism of Trp-cage unfolding. The process starts with a destabilizing proline shift in the hydrophobic core of the miniprotein, followed by a gradual destruction of the hydrophobic loop and the α-helix. Despite differences in interactions of urea vs guanidinium with various peptide moieties, the overall destabilizing action of these two denaturants on Trp-cage is very similar.
    Keywords: Guanidine -- Chemistry ; Tryptophan -- Chemistry ; Urea -- Chemistry
    ISSN: 15206106
    E-ISSN: 1520-5207
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 8
    Language: English
    In: The journal of physical chemistry. B, 03 November 2011, Vol.115(43), pp.12521-6
    Description: The behavior of guanidinium chloride at the surface of aqueous solutions is investigated using classical molecular dynamics (MD) simulations. It is found that the population of guanidinium ions oriented parallel to the interface is greater in the surface region than in bulk. The opposite is true for ions in other orientations. Overall, guanidinium chloride is depleted in the surface region, in agreement with the fact that the addition of guanidinium chloride increases the surface tension of water. The orientational dependence of the surface affinity of the guanidinium cation is related to its anisotropic hydration. To bring the ion to the surface in the parallel orientation does not require hydrogen bonds to be broken, in contrast to other orientations. The surface enrichment of parallel-oriented guanidinium indicates that its solvation is more favorable near the surface than in bulk solution for this orientation. The dependence of the bulk and surface properties of guanidinium on the force field parameters is also investigated. Despite significant quantitative differences between the force fields, the surface behavior is qualitatively robust. The implications for the orientations of the guanidinium groups of arginine side chains on protein surfaces are also outlined.
    Keywords: Guanidine -- Chemistry ; Water -- Chemistry
    E-ISSN: 1520-5207
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 9
    Language: English
    In: The journal of physical chemistry. B, 30 May 2013, Vol.117(21), pp.6394-402
    Description: Cationic specificity which follows the Hofmeister series has been established for the catalytic efficiency of haloalkane dehalogenase LinB by a combination of molecular dynamics simulations and enzyme kinetic experiments. Simulations provided a detailed molecular picture of cation interactions with negatively charged residues on the protein surface, particularly at the tunnel mouth leading to the enzyme active site. On the basis of the binding affinities, cations were ordered as Na(+) 〉 K(+) 〉 Rb(+) 〉 Cs(+). In agreement with this result, a steady-state kinetic analysis disclosed that the smaller alkali cations influence formation and productivity of enzyme-substrate complexes more efficiently than the larger ones. A subsequent systematic investigation of two LinB mutants with engineered charge in the cation-binding site revealed that the observed cation affinities are enhanced by increasing the number of negatively charged residues at the tunnel mouth, and vice versa, reduced by decreasing this number. However, the cation-specific effects are overwhelmed by strong electrostatic interactions in the former case. Interestingly, the substrate inhibition of the mutant LinB L177D in the presence of chloride salts was 7 times lower than that of LinB wild type in glycine buffer. Our work provides new insight into the mechanisms of specific cation effects on enzyme activity and suggests a potential strategy for suppression of substrate inhibition by the combination of protein and medium engineering.
    Keywords: Hydrolases -- Chemistry
    ISSN: 15206106
    E-ISSN: 1520-5207
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 10
    Language: English
    In: The Journal of Chemical Physics, 28 December 2015, Vol.143(24)
    Description: We study statistical copolymerization effects on the upper critical solution temperature (CST) of generic homopolymers by means of coarse-grained Langevin dynamics computer simulations and mean-field theory. Our systematic investigation reveals that the CST can change monotonically or non-monotonically with copolymerization, as observed in experimental studies, depending on the degree of non-additivity of the monomer (A-B) cross-interactions. The simulation findings are confirmed and qualitatively explained by a combination of a two-component Flory-de Gennes model for polymer collapse and a simple thermodynamic expansion approach. Our findings provide some rationale behind the effects of copolymerization and may be helpful for tuning CST behavior of polymers in soft material design.
    Keywords: Special Topic: Coarse Graining Of Macromolecules, Biopolymers, And Membranes
    ISSN: 0021-9606
    E-ISSN: 1089-7690
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
Close ⊗
This website uses cookies and the analysis tool Matomo. Further information can be found on the KOBV privacy pages