Showing papers in "Biophysical Chemistry in 2011"

TL;DR: 1:1 correspondence between predicted and measured m-values covering a range of 12 kcal/mol/M in protein stability for 46 proteins and 9 different osmolytes is shown.

TL;DR: The current understanding of the features that control metal specificity of the allosteric response in these systems are discussed, and the role that structure, thermodynamics and conformational dynamics play in mediating allosterics activation or inhibition of DNA binding is discussed.

TL;DR: The homogeneous nucleation model is inherently robust and is unlikely to yield fractional values if the underlying process is strictly homogeneous with a free energy profile G(n) that displays a sharp maximum at n=n*, where n* corresponds to the critical nucleus.

TL;DR: The emerging principles from this ensemble view of proteins have proven surprisingly useful in describing the role of intrinsic disorder in inter-domain communication, functional adaptation mediated by mutational control of fluctuations, and evolutionary conservation of the energetics of protein stability.

TL;DR: The structure, properties and growth of columnar (gastropod) nacre is reported on with emphasis on the genus Haliotis in contrast to sheet nacre of many bivalves.

TL;DR: The PT band of PDOHBA is found to be an excellent reporter for the mapping of destructive and protective behavior of SDS with variation of chaotrope concentration and indicates the spontaneity of this probe-protein complexation process.

TL;DR: These novel simulations provide a more detailed understanding of low molecular-weight polymer-siRNA behavior, mimicking the endosomal environment and provide input of direct relevance to the "proton sponge theory", thereby advancing the rational design of non-viral gene delivery systems.

TL;DR: This review introduces the use of static uniaxially oriented samples results in angular constraints which also provide information for the detailed analysis of polypeptide structures and ongoing developments combining solid-state NMRSpectroscopy with information from solution NMR spectroscopy and molecular modelling as well as exploratory studies using dynamic nuclear polarization solid- state NMR will be presented.

TL;DR: Biochemical thermodynamics is also important in enzyme kinetics because apparent equilibrium constant K' can be calculated from experimentally determined kinetic parameters when initial velocities have been determined for both forward and reverse reactions.

TL;DR: A novel chaperone function for the periplasmic domain of OmpA that may be relevant for folding in vivo is identified and extensively investigated the properties of the self-association reaction of unfolded Ompa.

TL;DR: Conformational properties of the full-length human and rat islet amyloid polypeptide 1-37 were studied at 310 and 330 K by MD simulations both for the cysteine (reduced IAPP) and cystine (oxidized I APP) moieties.

TL;DR: Thermodynamic parameters for the melting, and the effect of the co-solvent in determining a change in thermal stability of the protein were evaluated and kinetic information was obtained showing that both unfolded and folded states of lysozyme act as reactants for the clustering event.

TL;DR: This work presents results from the theoretical simulations of catalytic mechanism at the two-step successive surface redox reaction under conditions of square-wave voltammetry, and gives set of qualitative criteria to distinguish this mechanism from similar ones studied under voltammetric conditions.

TL;DR: This paper outlines the theory for periodic solutions to the wave equation and compares these results to action potentials from the femoral nerve of the locust and describes the frequently occurring minimum-distance doublet pulses seen in these neurons and compare them to the periodic pulse solutions.

TL;DR: Molecular docking and electrostatic surface potential calculations reveal contrasting binding modes of fisetin and 3-HF with HbA.

TL;DR: The results presented demonstrate the usefulness of FRAP to access the fast binding kinetics characteristic of cellulases operating at their optimal temperature.

TL;DR: A structural mechanism for calcium-dependent conformational change in which the linker between CTT sites A and C buckles to form an A-C hairpin that is bridged by calcium-saturated CaM is proposed.

TL;DR: 2,6-bis(1H-benzimidazol-2-yl)pyridine (BBP), which is almost non-fluorescent in aqueous solutions, reveals a strong emission enhancement in a hydrophobic environment of a phospholipid bilayer, making it interesting for fluorescence probing of water content in a lipid membrane.

TL;DR: This review presents an overview of recent advances in the field, focusing on both the theoretical and the experimental developments, and outlines the strategy for future volumetric studies that will result in new insights into the old problem of interactions of proteins with protecting and denaturing osmolytes.

TL;DR: The results indicate that low-lying excited state conformers of hen lysozyme are characterized by slowly fluctuating local conformations around these cavities, attributed to the opportunities for water molecules to penetrate into the cavities.

TL;DR: Tripleplex folding is driven almost entirely by the energy of cation binding with little or no contribution from other weak molecular interactions.

TL;DR: Data on protein folding, ligand binding processes, and phospholipid phase transitions is reviewed, together with discussion of interpretation and further significant applications.

TL;DR: This study shows that articaine has an additional unique lipophilicity switch in its ability to form an intramolecular hydrogen bond which may enhance its diffusion through membranes and connective tissue.

TL;DR: Evidence provided by the decomposition of absorption spectra, fluorescence decay components, fluorescent energy transfer and induced CD signals reveals that peptide conjugates of di- and tricationic porphyrins bind to DNA by two distinct binding modes which can be identified as intercalation and external binding.

TL;DR: This work investigates the local structure of hydration water molecules as a function of the distance from the protein and water molecules respectively in 188 high resolution protein structures and compares it with those obtained from molecular dynamics simulations.

TL;DR: Results showed that both FF and FH dimers form stable guanine quadruplexes in the presence of potassium ions like those in Fibri, and the thermal stability of aptamer dimers was slightly lower compared to those of canonical aptamers, but sufficient for practical applications.

TL;DR: No self-structure formation was observed in poly(A) with both daunomycin and aristololactam-β-D-glucoside suggesting the hindrance of the sugar moiety for such structural organization.

TL;DR: The results presented herein suggest that some proteins that only undergo significant conformational changes around active sites have a relatively high probability of being involved in an actual conformational change and may help solve the flexible-docking problem of a protein with another molecule.

TL;DR: It is proposed that transient, predominantly electrostatic interactions between glycosaminoglycans and the precursor proteins mediate the acceleration of fibril formation in vitro.

TL;DR: The findings suggest that myricetin interacts with soluble Aβ via two mechanisms, association with the hydrophobic C-terminal region and interactions with the aromatic side chains.