Thermodynamic and structural characterization of Asn and Ala residues in the disallowed II' region of the Ramachandran plot

Residue Asn47 at position L1 of a type II' beta-turn of the alpha-spectrin SH3 domain is located in a disallowed region of the Ramachandran plot (phi = 56 +/- 12, psi = -118 +/- 17). Therefore, it is expected that replacement of Asn47 by Gly should result in a considerable stabilization of the protein. Thermodynamic analysis of the N47G and N47A mutants shows that the change in free energy is small (approximately 0.7 kcal/mol; approximately 3 kJ/mol) and comparable to that found when mutating a Gly to Ala in a alpha-helix or beta-sheet. X-ray structural analysis of these mutants shows that the conformation of the beta-turn does not change upon mutation and, therefore, that there is no relaxation of the structure, nor is there any gain or loss of interactions that could explain the small energy change. Our results indicate that the energetic definition of II' region of the Ramachandran plot (phi = 60 +/- 30, psi = -115 +/- 15) should be revised for at least Ala and Asn in structure validation and protein design.     

Internal motional amplitudes and correlated bond rotations in an alpha-helical peptide derived from 13C and 15N NMR relaxation

Peptide GFSKAELAKARAAKRGGY folds in an alpha-helical conformation that is stabilized by formation of a hydrophobic staple motif and an N-terminal capping box (Munoz V. Blanco FJ, Serrano L, 1995, Struct Biol 2:380-385). To investigate backbone and side-chain internal motions within the helix and hydrophobic staple, residues F2, A5, L7, A8, and A10 were selectively 13C- and 15N-enriched and NMR relaxation experiments were performed in water and in water/trifluoroethanol (TFE) solution at four Larmor frequencies (62.5, 125, 150, and 200 MHz for 13C). Relaxation data were analyzed using the model free approach and an anisotropic diffusion model. In water, angular variances of motional vectors range from 10 to 20 degrees and backbone phi,psi bond rotations for helix residues A5, L7, A8, and A10 are correlated indicating the presence of Calpha-H, Calpha-Cbeta, and N-H rocking-type motions along the helix dipole axis. L7 side-chain CbetaH2 and CgammaH motions are also correlated and as motionally restricted as backbone CalphaH, suggesting considerable steric hindrance with neighboring groups. In TFE which stabilizes the fold, internal motional amplitudes are attenuated and rotational correlations are increased. For the side chain of hydrophobic staple residue F2, wobbling-in-a-cone type motions dominate in water, whereas in TFE, the Cbeta-Cgamma bond and phenyl ring fluctuate more simply about the Calpha-Cbeta bond. These data support the Daragan-Mayo model of correlated bond rotations (Daragan VA, Mayo KH, 1996, J Phys Chem 100:8378-8388) and contribute to a general understanding of internal motions in peptides and proteins.     

Experimental amebiasis: immunohistochemical study of immune cell populations

Distribution of immune cell populations was studied in a C3H/HeJ mouse model of intestinal amebiasis from 5 to 60 days post-inoculation with Entamoeba histolytica, using immunoperoxidase techniques. At various time intervals, the ceca from mice were fixed in 10% formalin, dehydrated, embedded and sectioned at 5 microm. Sections were incubated with conjugated peroxidase-labelled antibodies to mouse IgA, IgM, and IgG. Color was developed with 3, 3'-diaminobenzidine tetrahydrochloride (DAB)/H2O2 solution. CD3, CD4, and CD8 cells, as well as neutrophils were detected by reacting with biotin-conjugated anti-mouse CD3, CD4, CD8, and CD11 monoclonal antibodies, followed by their incubation with avidin-peroxidase and color development with DAB/H2O2 solution. Erythrocin B and toluidine blue were used to stain eosinophils and Mast cells, respectively. It was observed that the IgA+ plasma cell was the dominating immune cell present in the mucosa, although eosinophils, neutrophils, CD3+, CD4+, CD8+, IgM+, IgG+ cells and Mast cells were also seen. Results of this study suggest that infiltration of immune cells at the mucosal surface during intestinal amebiasis might be important in the defense against this parasite.     

The cell cycle inhibitor p21 controls T-cell proliferation and sex-linked lupus development

Here we show that the cell-cycle regulator p21 is involved in immune system function. T lymphocytes from p21-/- mice exhibit significant proliferative advantage over wild-type cells following prolonged stimulation, but not after primary activation. Consistent with this, p21-deficient mice accumulate abnormal amounts of CD4+ memory cells, and develop loss of tolerance towards nuclear antigens. Similar to human lupus, female p21-deficient mice develop antibodies against dsDNA, lymphadenopathy, and glomerulonephritis, leading to decreased viability. These data demonstrate a specialized role for p21 in the control of T-cell proliferation, tolerance to nuclear antigens, and female-prone lupus. These findings could be the basis for new therapeutic approaches to lupus.     

A novel target of lithium therapy

Phosphatases converting 3'-phosphoadenosine 5'-phosphate (PAP) into adenosine 5'-phosphate are of fundamental importance in living cells as the accumulation of PAP is toxic to several cellular systems. These enzymes are lithium-sensitive and we have characterized a human PAP phosphatase as a potential target of lithium therapy. A cDNA encoding a human enzyme was identified by data base screening, expressed in Escherichia coli and the 33 kDa protein purified to homogeneity. The enzyme exhibits high affinity for PAP (K(m)<1 microM) and is sensitive to subtherapeutic concentrations of lithium (IC(50)=0.3 mM). The human enzyme also hydrolyzes inositol-1, 4-bisphosphate with high affinity (K(m)=0.4 microM), therefore it can be considered as a dual specificity enzyme with high affinity (microM range) for both PAP and inositol-1,4-bisphosphate. Hydrolysis of inositol-1,4-bisphosphate was also inhibited by lithium (IC(50)=0.6 mM). Thus, we present experimental evidence for a novel target of lithium therapy, which could explain some of the side effects of this therapy.     

The SH3-fold family: experimental evidence and prediction of variations in the folding pathways

To investigate the relationships between protein topology, amino acid sequence and folding mechanisms, the folding transition state of the Sso7d protein has been characterised both experimentally and theoretically. Although Sso7d protein has a similar topology to that of the SH3 domains, the structure of its transition state is different from that of alpha-spectrin and src SH3 domains previously studied. The folding algorithm, Fold-X, including an energy function with specific sequence features, accounts for these differences and reproduces with a good agreement the set of experimental phi(double dagger-U) values obtained for the three proteins. Our analysis shows that taking into account sequence features underlying protein topology is critical for an accurate prediction of the folding process.     

Plasmalemma-associated malate dehydrogenase activity in onion root cells

Summary Plasma membrane vesicles isolated from onion roots showed oxaloacetate reductase activity as well as other oxidoreductase activities. Purification and further sequencing showed that the protein responsible for the activity is a 40 kDa protein which corresponds to the cytosolic soluble malate dehydrogenase. However, the activity remained bound to the membrane after repeated freezing and thawing cycles and further washing, excluding a cytosolic contamination as the source of the activity. Furthermore, a second 28 kDa protein has been copurified together with the 40 kDa protein. The plasmalemma oxaloacetate reductase activity shows both donor and acceptor sites located towards the cytoplasmic side of the plasma membrane. This enzyme catalyzed the oxidation of NADH by oxaloacetate and the reduction of NAD⁺ by malate in the presence of an oxaloacetate-withdrawing system. We conclude that a significant amount of the cytosolic malate dehydrogenase can be specifically attached to the cytosolic face of the plasmalemma. A possible role in a putative malate shuttle associated to the plasma membrane is discussed.Abbreviations AFR ascorbate free radical - DQ duroquinone - OA oxaloacetate - DPIP dichlorophenolindophenol - MDH malate dehydrogenase - PHMB p-hydroxymercuribenzoate     

Reaction of ethyl 2-amino-4,6-O-benzylidene-2-deoxy-d-gluconate with acetylenic esters

Ethyl 2-amino-4,6-O-benzylidene-2-deoxy-d-gluconate adds to acetylenic esters to give sugar enaminones. The following acetylene derivatives have been employed: methyl propiolate, ethyl phenylpropiolate, and dimethyl acetylenedicarboxylate (6). With compound 6, the reaction leads to a mixture of the expected enaminone and the isomeric oxazolidine derivative. The structures and configurations of the new compounds were studied by spectroscopic and chemical methods.     

The interaction between subunits in the tubulin dimer.

Limited proteolysis and chemical cross-linking techniques have been used to study the interaction between alpha- and beta-tubulin subunits. Trypsin digestion of tubulin dimer resulted in the cleavage of the alpha-subunit into two fragments, whereas chymotrypsin cleaved the beta-subunit into two distinct fragments. All of these fragments have been mapped on the tubulin subunits by further proteolysis with formic acid. Cross-linking of trypsin- and chymotrypsin-cleaved subunits has been performed with two different cross-linker agents of different cross-linking distance. The addition of formaldehyde resulted in the cross-linking of the alpha-tubulin N-terminal fragment with beta-tubulin C-terminal domain. The same result was obtained when methyl 4-mercaptobutyrimidate was used.