The thermodynamics of protein-ligand interaction and solvation: insights for ligand design

Isothermal titration calorimetry is able to provide accurate information on the thermodynamic contributions of enthalpy and entropy changes to free energies of binding. The Structure/Calorimetry of Reported Protein Interactions Online database of published isothermal titration calorimetry studies and structural information on the interactions between proteins and small-molecule ligands is used here to reveal general thermodynamic properties of protein-ligand interactions and to investigate correlations with changes in solvation. The overwhelming majority of interactions are found to be enthalpically favoured. Synthetic inhibitors and biological ligands form two distinct subpopulations in the data, with the former having greater average affinity due to more favourable entropy changes on binding. The greatest correlation is found between the binding free energy and apolar surface burial upon complex formation. However, the free-energy contribution per unit area buried is only 30-50% of that expected from earlier studies of transfer free energies of small molecules. A simple probability-based estimator for the maximal affinity of a binding site in terms of its apolar surface area is proposed. Polar surface area burial also contributes substantially to affinity but is difficult to express in terms of unit area due to the small variation in the amount of polar surface buried and a tendency for cancellation of its enthalpic and entropic contributions. Conventionally, the contribution of apolar desolvation to affinity is attributed to gain of entropy due to solvent release. Although data presented here are supportive of this notion, because the correlation of entropy change with apolar surface burial is relatively weak, it cannot, on present evidence, be confidently considered to be correct. Further, thermodynamic changes arising from small differences between ligands binding to individual proteins are relatively large and, in general, uncorrelated with changes in solvation, suggesting that trends identified across widely differing proteins are of limited use in explaining or predicting the effects of ligand modifications.     

Time-dependent evolution of tissue markers by MALDI-MS imaging

We have used MALDI-MS imaging (MALDI-MSI) to monitor the time dependent appearance and loss of signals when tissue slices are brought rapidly to room temperature for short to medium periods of time. Sections from mouse brain were cut in a cryostat microtome, placed on a MALDI target and allowed to warm to room temperature for 30 s to 3 h. Sections were then refrozen, fixed by ethanol treatment and analysed by MALDI-MSI. The intensity of a range of markers were seen to vary across the time course, both increasing and decreasing, with the intensity of some markers changing significantly within 30 s and markers also showed tissue location specific evolution. The markers resulting from this autolysis were compared directly to those that evolved in a comparable 16 h on-tissue trypsin digest, and the markers that evolved in the two studies were seen to be substantially different. These changes offer an important additional level of location-dependent information for mapping changes and seeking disease-dependent biomarkers in the tissue. They also indicate that considerable care is required to allow comparison of biomarkers between MALDI-MSI experiments and also has implications for the standard practice of thaw-mounting multiple tissue sections onto MALDI-MS targets.     

Identification and characterization of an essential telomeric repeat binding factor in fission yeast

Whereas mammalian cells harbor two double strand telomeric repeat binding factors, TRF1 and TRF2, the fission yeast Schizosaccharomyces pombe has been thought to harbor solely the TRF1/TRF2 ortholog Taz1p to perform comparable functions. Here we report the identification of telomeric repeat binding factor 1 (Tbf1), a second TRF1/TRF2 ortholog in S. pombe. Like the Taz1p, the identified Tbf1p shares amino acid sequence similarity, as well as structural and functional characteristics, with the mammalian TRF1 and TRF2 proteins. This family of proteins shares a common architecture with two separate structural domains. An N-terminal domain is necessary and sufficient for the formation of homodimers, and a C-terminal MYB/homeodomain mediates sequence specific recognition of double-stranded telomeric DNA. The identified Tbf1p binds S. pombe telomeric DNA with high sequence specificity in vitro. Targeted deletion of the tbf1 gene reveals that it is essential for survival, and overexpression of the tbf1 gene leads to telomere elongation in vivo, which is dependent upon the MYB domain. These data suggest that fission yeast, like mammals, have two factors that bind double-stranded telomeric DNA and perform distinct roles in telomere length regulation.     

Benzothiazole based inhibitors of p38alpha MAP kinase

Rational design, synthesis, and SAR studies of a novel class of benzothiazole based inhibitors of p38alpha MAP kinase are described. The issue of metabolic instability associated with vicinal phenyl, benzo[d]thiazol-6-yl oxazoles/imidazoles was addressed by the replacement of the central oxazole or imidazole ring with an aminopyrazole system. The proposed binding mode of this new class of p38alpha inhibitors was confirmed by X-ray crystallographic studies of a representative inhibitor (6a) bound to the p38alpha enzyme.     

Morphology of the nematocysts of the medusae of two scyphozoans, Catostylus mosaicus and Phyllorhiza punctata (Rhizostomeae): implications for capture of prey

Abstract. We examined the cnidomes (total complement of nematocysts) of medusae of the zooxanthellate and azooxanthellate jellyfishes Phyllorhiza punctata and Catostylus mosaicus (Rhizostomeae, Scyphozoa), and compared the assemblage of zooplankton captured on the oral arms of each species to determine whether differences in the types or amount of zooplankton captured were consistent with possible differences in the cnidomes. Cnidomes were described using light and scanning electron microscopy. Each species had a distinct cnidome and, in general, specimens of P. punctata appeared to have far fewer nematocysts than those of C. mosaicus. Four types of nematocysts were identified in medusae of C. mosaicus; 2 types of holotrichous isorhizae, rhopaloids, and birhopaloids. In C. mosaicus, the oral arms and bell margins possessed all of these types, but the cnidomes of the 2 regions differed in relative abundances and sizes of isorhizae and rhopaloids. Five types of nematocysts were identified in medusae of P. punctata, although not all types were found in all specimens. Round holotrichous isorhizae were found only in the bell, while oval holotrichous isorhizae, rhopaloids of 2 distinct size ranges, and birhopaloids were found in the bell and oral arms. Cnidomes of the bell and oral arms in specimens of P. punctata also differed in the relative abundance and sizes of oval isorhizae and rhopaloids. Although there were clear differences in the overall cnidomes and absolute abundances of nematocysts in each species, the oral arms (feeding appendages) of specimens of both C. mosaicus and P. punctata had similar types and relative abundances of nematocysts. Zooplankton sampled from the oral arms of each species showed that both species preyed predominantly on copepod nauplii and larvae of gastropods and bivalves. Medusae of C. mosaicus captured ～10 × more gastropod larvae and 5 × more bivalve larvae than those of P. punctata. Specimens of P. punctata captured approximately twice as many copepod nauplii as those of C. mosaicus. Differences in the relative abundance of types of zooplankton captured by each species could not be adequately explained by differences in the cnidomes of the oral arms.     

Nuclear-magnetic-resonance studies of Pseudomonas aeruginosa cytochrome c-551.

Nuclear magnetic resonance (NMR) spectroscopy was used to study Pseudomonas aeruginosa cytochrome c-551. Assignments of resonances to specific residues have been made. A low-resolution X-ray structure was used to aid assignments. A structural comparison was made between P. aeruginosa cytochrome c-551 and mammalian cytochrome c, based on comparisons of NMR data.     

Cell wall elastic constitutive laws and stress-strain behavior of plant vegetative tissue

The appropriateness of several elastic constitutive laws for apple and potato cell walls is tested using uniform cell inflation data. Whole-tissue stress-strain behavior under uniaxial loading is predicted from an analysis of the compression of a conglomerate of cells in a simple arrangement.     

Quantification of polyacrylamide gel bands by digital image processing

A method of quantifying bands on polyacrylamide gels based on image processing of digitized photographic negatives is presented.