Showing papers in "Biophysical Chemistry in 2014"

TL;DR: This paper describes a kinetic method that, at least in some cases, unequivocally distinguishes induced fit from conformational selection and provides examples from the literature and discusses the limitations.

TL;DR: A number of recent advances in computer-aided drug discovery techniques that have been proposed to incorporate receptor flexibility into structure-based drug design help to improve the accuracy of methods used to estimate binding affinities and can contribute to the discovery of novel drug leads.

TL;DR: In this article, it was shown that induced fit is always sufficient and often necessary to account for the relaxation kinetics of ligand binding to a biological macromolecule and is therefore an essential component of any binding mechanism.

TL;DR: It is suggested that conformational selection takes place not once in a given binding/allosteric event, but at every step along the allosteric pathway.

TL;DR: The results indicate that the volume occupied by the crowding agent, but not its size, plays an important role on the initial velocity of reactions involving tiny enzymes, while the enzyme size is another important factor influencing the velocity of the reactions of large enzymes occurring in Dextran crowded media.

TL;DR: New insights from single molecule studies are surveyed that advance the understanding of the molecular mechanisms underlying biomolecular recognition, including induced fit and conformational selection.

TL;DR: The extension and the temperature behavior of the boundary region, its structure and composition are discussed in detail, using the example of a molecular dynamics model of an aqueous solution of the human amyloid polypeptide, hIAPP.

TL;DR: Support of molecular docking results by biochemical fluorescence experiments confirms the validity of docking calculation and indicates that NG can interact with BLG without affecting the secondary structure of protein.

TL;DR: Recent developments in the use of paramagnetic relaxation enhancement to directly study sparsely-populated states of proteins are summarized and it is suggested that the existence of partially-closed states in the absence of ligand facilitates the transition to the closed ligand-bound state.

TL;DR: Results showed that with increasing cholesterol concentration in the bilayer, the free energy barrier for translocation of 5-FU across the bilay also increases which can be attributed to the condensing effect of the cholesterol on the bilayers.

TL;DR: It has been found that the stability of ion pairs formed by the carboxylate group and added inorganic cations decreases in the sequence Mg( 2+)>Ca(2+)>Na(+)>K(+) and all formed ion pairs are weak and decrease in stability with increasing salt concentration.

TL;DR: It is found that the choice of atomic partial charges can have a significant impact on the quantitative results, meaning that careful validation of parameters for new drugs, such as performed here, should be performed prior to their use in biomolecular simulations.

TL;DR: In this paper, the authors report synergy in the glycine betaine (GB) and urea mixture by using a model peptide and show that in the GB-urea mixture, GB acts as a stronger osmolyte and Urea becomes a weaker denaturing agent.

TL;DR: In this work, Δ(R)g(+) values for the enzymatic G6P isomerization were determined as a function of the G 6P equilibrium molality between 25 °C and 37 °C, and the influence of the buffer and of potassium glutamate as an additive on the reaction equilibrium was measured and predicted with ePC-SAFT in good agreement.

TL;DR: The viability of using synchrotron-based full-field infrared imaging to study biochemical processes inside living cells is successfully tested and a description of cellular biochemistry and biophysics that contains both spatial and temporal information is given.

TL;DR: Thermal unfolding of ribonuclease A (RNase) was analyzed in various osmolyte solutions of glycine, proline, sarcosine, N,N-dimethylglycine, betaine, myo-inositol, taurine, and trimethylamine-N-oxide and the Wyman-Tanford plot could be integrated to calculate the stabilization free energy of the protein (∆∆G) in the solution.

TL;DR: Relatively small changes in the absorption spectrum when forming the complexes with the G-quadruplex, the positive CD signal, and the large accessibility of the I(-) quencher, suggested that all these porphyrins are not intercalated between theG-quartet.

TL;DR: This work studied spheroidal nanoparticles made from bovine α-lactalbumin cross-linked with glutaraldehyde in the presence of acetone to study the conformational changes that proteins undergo during the assembly process.

TL;DR: An investigation of the hydration dependence of myoglobin dynamics and the relevance of protein+hydration water relaxations and of the thermodynamic state of hydration water to the onset of the protein dynamical transition is discussed.

TL;DR: This study characterized an unknown protein (ACYPI39568) that was predicted to be enriched in the salivary glands of pea aphid and belongs to an aphid-specific, cysteine-rich protein family that contains 14 conserved cysteines.

TL;DR: These studies build upon previously theorized interactions, yielding a more comprehensive model of binding between estrogens and HA, as well as demonstrate the value of the confluence of biochemical assay methods with analytical NMR techniques.

TL;DR: It is demonstrated that single-molecule FRET can be used to probe the structures of a flexible ssDNA and it is found that three of the ssDNAs with lengths shorter than the persistence length are indeed long enough to undergo folding.

TL;DR: The behavior under tension of the native state (N), and that of the ensemble of partially folded (PF) conformations the protein visits en route to N, are characterized, which collectively act as a long-lived state controlling the slow kinetic phase of the folding process.

TL;DR: The homopolymer of hepatitis C virus, protein p7 of strain 1a, which is known to form channels, is used to investigate the dynamics of physiological relevant ions, Na(+, K(+), Cl(-) and Ca(2+) in the vicinity of the protein bundle.

TL;DR: This report is the first evidencing that Thermomyces lanuginosus lipase co-exists as stable dimeric and monomeric forms in solution.

TL;DR: It is suggested that TMAO-dependent stabilization of actin structure facilitates the binding of G- form actin to the ends of F-form actin filaments, whereas the binding between ends of mature filaments was impaired by T MAO.

TL;DR: The porphyrazines as the complexes that bind to the G-quadruplex DNA, could be suitable candidates for further investigations about inhibition of telomerase enzyme.

TL;DR: The spectroscopic study shows that the aggregation tendency is enhanced with increased glutamine repeat expansion and that the concentration plays another critical factor in the β-sheet formation.

TL;DR: The ability to monitor DNA supercoiling at high temperature and the possibility to perform magnetic tweezers assays on thermophilic systems are demonstrated and the results imply that average in vivo DNA tensions range between 0.3 and 1.1 pN.

TL;DR: Essential dynamics reveal that overall motions of WT and W32F are mainly involved in three to four eigenvectors, but in H43R the overall motions are mainly in the first eigenvector, which provides a unifying description for the structural destabilization, enhanced peroxidase activity, loss of dismutation activity and increase in aggregation propensity in the pathology of fALS diseases.