Biochemical functions of proteins in cells frequently involve interactions with various ligands. Proteomic methods for the identification of proteins that interact with specific ligands such as metabolites, signaling molecules, and drugs are valuable in investigating the regulatory mechanisms of cellular metabolism, annotating proteins with unknown functions, and elucidating pharmacological mec...

The binding of low-molecular-weight heparin to an amino-terminal-truncated, 132-amino-acid, human acidic fibroblast growth factor form has been studied by isothermal titration calorimetry. This technique yields values for the enthalpy change and equilibrium constant, from which the Gibbs energy and entropy change are also calculated. Experiments in different buffers and pH values show that the ...

H igh-resolution structures of proteins and their complexes are now appearing in the Research Collaboratory for Structural Bioinformatics (RCSB) database at a tremendous rate. When analyzing the structures of proteins, it is often tempting to try to extract energetic contributions to stability or binding interactions. However, as many experiments have shown, some specific interactions that look...

The formation of halogen bonds from iodopentafluorobenzene and 1-iodoperfluorohexane to a series of bis(η(5)-cyclopentadienyl)metal hydrides (Cp2TaH3, 1; Cp2MH2, M = Mo, 2, M = W, 3; Cp2ReH, 4; Cp2Ta(H)CO, 5; Cp = η(5)-cyclopentadienyl) is demonstrated by (1)H NMR spectroscopy. Interaction enthalpies and entropies for complex 1 with C6F5I and C6F13I are reported (ΔH° = -10.9 ± 0.4 and -11.8 ± 0...

Stably folded membrane proteins reside in a free energy minimum determined by the interactions of the peptide chains with each other, the lipid bilayer hydrocarbon core, the bilayer interface, and with water. The prediction of three-dimensional structure from sequence requires a detailed understanding of these interactions. Progress toward this objective is summarized in this review by means of...

The Fab portion of a humanized antibody (Fab-12; IgG form known as rhuMAb VEGF) to vascular endothelial growth factor (VEGF) has been affinity-matured through complementarity-determining region (CDR) mutation, followed by affinity selection using monovalent phage display. After stringent binding selections at 37 degrees C, with dissociation (off-rate) selection periods of several days, high aff...

Proteins with multiple binding sites exhibit a complex behavior that depends on the intrinsic affinities for each site and the energetic communication between the sites. The contributions from intrinsic affinity and cooperativity are difficult to deconvolute using conventional binding experiments that lack information about the occupancies of individual sites. Here, we report the concerted use ...

Studies of the binding and bending of the AdMLP TATA sequence (TATAAAAG) by the core domain of yeast TBP allow quantitation of the roles of the N-terminal domains of yeast and human TBP. All three proteins bind DNA via a three-step mechanism with no evidence for an initially bound but unbent DNA. The large enthalpy and entropy of activation for the first step in yTBP binding can now be assigned...

Abstract Proton-exchange membrane fuel cells demand efficient electrode–electrolyte interfaces to catalyse the oxygen reduction reaction (ORR), kinetics of which depends on energetics surface adsorption and electrolyte environment. Here we show an unanticipated effect non-specifically adsorbed anions ORR a Pt(111) electrode; these trends do not follow usual descriptor, that is *OH binding energ...