The solution structure of the domain from MeCP2 that binds to methylated DNA.

MeCP2 is an abundant mammalian protein that binds methylated CpG (mCpG) sequences within double-stranded DNA, represses transcription by recruiting histone deacetylases, and is essential for embryonic development. It is one of a family of proteins which mediate the biological consequences of DNA methylation. These proteins each possess a sequence motif of about 70 residues which, in MeCP2, form a domain necessary and sufficient for binding to mCpG. The solution structure of the mCpG-binding domain (MBD) from MeCP2 has been solved and the DNA-binding surface of the domain mapped using NMR spectroscopy. Residues 95-162 of MeCP2 adopt a novel fold forming a wedge-shaped structure. An N-terminal four-stranded antiparallel beta-sheet forms one face of the wedge, while the other face is formed mainly by a C-terminal helical region. The thin end of the wedge is extended by a long loop between beta-strands B and C containing many basic residues. The B-C loop together with residues in strands B, C and D, and at the N terminus of the alpha-helix, appears to form an interface with methylated DNA. Unstructured residues at the NH2 terminus of the domain are also involved in formation of the complex. The presence of numerous arginine and lysine side-chains on the DNA-binding surface of MBD is consistent with the requirement for the mCpG site to be flanked by non-specific sequences of base-pairs. The absence of symmetry in the domain implies that recognition does not exploit the symmetry of the binding site. A conserved hydrophobic pocket containing the side-chains of Tyr123 and Ile125 on the positively charged beta-sheet face is a candidate for the region of contact with the methyl-groups of the modified cytosine residues.

The solution structure of the complex of Lactobacillus casei dihydrofolate reductase with methotrexate.

We have determined the three-dimensional solution structure of the complex of Lactobacillus casei dihydrofolate reductase (18.3 kDa, 162 amino acid residues) formed with the anticancer drug methotrexate using 2531 distance, 361 dihedral angle and 48 hydrogen bond restraints obtained from analysis of multidimensional NMR spectra. Simulated annealing calculations produced a family of 21 structures fully consistent with the constraints. The structure has four alpha-helices and eight beta-strands with two other regions, comprising residues 11 to 14 and 126 to 127, also interacting with each other in a beta-sheet manner. The methotrexate binding site is very well defined and the structure around its glutamate moiety was improved by including restraints reflecting the previously determined specific interactions between the glutamate alpha-carboxylate group with Arg57 and the gamma-carboxylate group with His28. The overall fold of the binary complex in solution is very similar to that observed in the X-ray studies of the ternary complex of L. casei dihydrofolate reductase formed with methotrexate and NADPH (the structures of the binary and ternary complexes have a root-mean-square difference over the backbone atoms of 0.97 A). Thus no major conformational change takes place when NADPH binds to the binary complex. In the binary complex, the loop comprising residues 9 to 23 which forms part of the active site has been shown to be in the "closed" conformation as defined by M. R. Sawaya & J. Kraut, who considered the corresponding loops in crystal structures of complexes of dihydrofolate reductases from several organisms. Thus the absence of the NADPH does not result in the "occluded" form of the loop as seen in crystal studies of some other dihydrofolate reductases in the absence of coenzyme. Some regions of the structure in the binary complex which form interaction sites for NADPH are less well defined than other regions. However, in general terms, the NADPH binding site appears to be essentially pre-formed in the binary complex. This may contribute to the tighter binding of coenzyme in the presence of methotrexate.

Determination of stereospecific assignments, torsion-angle constraints, and rotamer populations in proteins using the program AngleSearch.

A general program, AngleSearch, which calculates coupling constants and interproton distances for any molecular fragment and does a grid search to find torsion angles, rotamer populations, and stereospecific assignments which fit the measured data has been developed. The program takes full advantage of the fact that ratios of cross-peak intensities (measured in HNHB and HN(CO)HB experiments) can provide accurate ratios of coupling constants even for large molecules. AngleSearch is capable of: (a) analyzing any type of residue including protein, RNA, DNA, and ligand residues; (b) conformational grid searching in dihedral-angle space using 6 degree steps; (c) averaging coupling constants and (l/r6) distances for rotamers undergoing fast exchange; (d) grid or Monte Carlo searching for populations of staggered rotamers; (e) using all available distance-related data from ROESY and/or NOESY spectra; (f) using any available coupling constant data having known relationships to corresponding dihedral angles; and (g) directly using cross-peak intensities related to values of coupling constants. The program can also assist in the stereospecific assignment of the alpha-CH2 protons of glycine residues. The effects of the quality of the input data on the results of the AngleSearch calculations have been assessed.

Distinct immunoreactivities suggest the existence of potential tissue variants in rat lipoprotein lipase.

Lipoprotein lipases (LPL) isolated from rat cardiac muscle and bovine milk were each used as immunogens to produce polyclonal anti-LPL sera and two anti-LPL monoclonal antibodies. The immunological reactivities of these antibody sources with LPL purified from rat cardiac muscle, lung, adipose tissue, mammary gland and skeletal muscle were compared by an e.l.i.s.a. and by Western blotting. Differences between the immunoreactivities of LPL from the distinct tissue sources were revealed in both systems. A synthetic peptide with a sequence corresponding to the heparin-binding site of LPL (Ser-Arg-Thr-Asn-Thr-Lys-Val-Ser-Arg-Ile-Thr-Gly-Leu) was produced and used as an immunogen. The antiserum produced against the synthetic peptide was found to bind specifically to the region of the heparin-binding site, as determined by use of a competition e.l.i.s.a. In use against the five tissue LPL preparations, this antiserum revealed only minor variations between the tissue sources, compared with the hierarchy of reactivity observed when antibodies raised against the whole molecule were used. In combination with the outcome of previous studies on some of the physical properties of these preparations [Soteriou and Cryer (1993) Int. J. Biochem. 25, 1483-1490], the observations reported here on the distinct immunoreactivities exhibited by LPL prepared from the different tissue sources of a single species indicate the necessity to characterize fully the nature of these differences.

Titin folding energy and elasticity.

Molecules of the giant protein titin are responsible for the passive elasticity and central A-band location of muscle myofibrils. The molecular mechanism of titin elasticity is not known, but the I-band region of the molecule appears capable of approximately fourfold reversible extension. Such large extensions are likely to involve unfolding of titin domains. In the present experiments, equilibrium unfolding of titin from rabbit skeletal muscles was studied in vitro by fluorescence and circular dichroism spectroscopy, after addition of guanidinium chloride. The data suggest two unfolding transitions, both of which appear cooperative. The second transition is likely to involve complete unfolding of the immunoglobulin- and fibronectin-like domains from which the molecules is composed. The free energy associated with this transition is comparable with the energy required to extend titin molecules to the maximum amount seen in situ.

Purification and characterization of lipoprotein lipase from the white adipose, skeletal muscle, cardiac muscle, mammary gland and lung tissues of the rat.

1. Lipoprotein lipase (LPL) was isolated from five rat tissues: white adipose, skeletal muscle, cardiac muscle, mammary gland and lung. 2. Specific activity of the preparations varied from 75 U/mg for skeletal muscle and 720 U/mg for adipose. 3. The preparations were further analysed using SDS-PAGE and a single component identified. The mol. wt of 61,000 Da of this component was consistent for all five of the tissue sources. 4. Significant differences in the values of the isoelectric points of the enzyme species were revealed. The values varied from 7.23 (SEM 0.022) for cardiac and lung to 7.51 (SEM 0.037) for mammary. 5. Two-dimensional electrophoresis, using isoelectric focusing in the first dimension and SDS-PAGE in the second revealed differences in the patterns of stained material derived from the five tissue sources.

Stereospecific assignments of the leucine methyl resonances in the 1H NMR spectrum of Lactobacillus casei dihydrofolate reductase.

A general method is described for the stereospecific assignment of methyl resonances in protein NMR spectra based on selective deuteration procedures. A selectively deuterated dihydrofolate reductase from L. casei was prepared by incorporating stereoselectively deuterated L-leucine, (2S,4R)[5,5,5-2H3]leucine. By comparing the COSY spectra of the dihydrofolate reductase-methotrexate complexes formed using deuterated and non-deuterated enzyme the stereospecific assignments for resonances of all 13 leucine residues were obtained by noting the absence of cross-peaks in spectra from the deuterated proteins.

A survey of interactions made by the giant protein titin.

A simple solid-phase binding assay was used to screen for interactions that the giant myofibrillar protein titin makes with other sarcomeric proteins. The titin used in the tests was purified by a modified procedure that results in isolation of approximately 20 mg relatively undegraded protein in < 24 h. In addition to the approximately 3 MDa polypeptide, bands at approximately 160 kDa and approximately 100 kDa were also consistently seen on gels. Binding of titin to myosin, C-protein, X-protein and AMP-deaminase was observed. The interaction with myosin appears to be with the light meromyosin part of the molecule.