Crystal structure of the complex of the cyclin D-dependent kinase Cdk6 bound to the cell-cycle inhibitor p19INK4d.

The crystal structure of the cyclin D-dependent kinase Cdk6 bound to the p19 INK4d protein has been determined at 1.9 A resolution. The results provide the first structural information for a cyclin D-dependent protein kinase and show how the INK4 family of CDK inhibitors bind. The structure indicates that the conformational changes induced by p19INK4d inhibit both productive binding of ATP and the cyclin-induced rearrangement of the kinase from an inactive to an active conformation. The structure also shows how binding of an INK4 inhibitor would prevent binding of p27Kip1, resulting in its redistribution to other CDKs. Identification of the critical residues involved in the interaction explains how mutations in Cdk4 and p16INK4a result in loss of kinase inhibition and cancer.

Structure of the cyclin-dependent kinase inhibitor p19Ink4d.

In cancer, the biochemical pathways that are dominated by the two tumour-suppressor proteins, p53 and Rb, are the most frequently disrupted. Cyclin D-dependent kinases phosphorylate Rb to control its activity and they are, in turn, specifically inhibited by the Ink4 family of cyclin-dependent kinase inhibitors (CDKIs) which cause arrest at the G1 phase of the cell cycle. Mutations in Rb, cyclin D1, its catalytic subunit Cdk4, and the CDKI p16Ink4a, which alter the protein or its level of expression, are all strongly implicated in cancer. This suggests that the Rb 'pathway' is of particular importance. Here we report the structure of the p19Ink4d protein, determined by NMR spectroscopy. The structure indicates that most mutations to the p16Ink4a gene, which result in loss of function, are due to incorrectly folded and/or insoluble proteins. We propose a model for the interaction of Ink4 proteins with D-type cyclin-Cdk4/6 complexes that might provide a basis for the design of therapeutics against cancer. The sequences of the Ink4 family of CDKIs are highly conserved

Structure of the chromatin binding (chromo) domain from mouse modifier protein 1.

The structure of a chromatin binding domain from mouse chromatin modifier protein 1 (MoMOD1) was determined using nuclear magnetic resonance (NMR) spectroscopy. The protein consists of an N-terminal three-stranded anti-parallel beta-sheet which folds against a C-terminal alpha-helix. The structure reveals an unexpected homology to two archaebacterial DNA binding proteins which are also involved in chromatin structure. Structural comparisons suggest that chromo domains, of which more than 40 are now known, act as protein interaction motifs and that the MoMOD1 protein acts as an adaptor mediating interactions between different proteins.

Transforming growth factor beta 1: three-dimensional structure in solution and comparison with the X-ray structure of transforming growth factor beta 2.

The three-dimensional solution structure of human transforming growth factor beta 1 (TGF-beta 1) has been determined using multinuclear magnetic resonance spectroscopy and a hybrid distance geometry/ simulated annealing algorithm. It represents one of the first examples of a mammalian protein structure that has been solved by isotopic labeling of the protein in a eukaryotic cell line and multinuclear NMR spectroscopy. The solution structure of the 25 kDa disulfide-linked TGF-beta 1 homodimer was calculated from over 3200 distance and dihedral angle restraints. The final ensemble of 33 accepted structures had no NOE or dihedral angle violations greater than 0.30 A and 5.0 degrees, respectively. The RMSD of backbone atoms for the ensemble of 33 structures relative to their mean structure was 1.1 A when all residues were used in the alignment and 0.7 A when loop regions were omitted. The solution structure of TGF-beta 1 follows two independently determined crystal structures of TGF-beta 2 (Daopin et al., 1992, 1993; Schlunegger & Grütter, 1992, 1993), providing the first opportunity to examine structural differences between the two isoforms at the molecular level. Although the structures are very similar, with an RMSD in backbone atom positions of 1.4 A when loop regions are omitted in the alignment and 1.9 A when all residues are considered, there are several notable differences in structure and flexibility which may be related to function. The clearest example of these is in the beta-turn from residues 69-72: the turn type found in the solution structure of TGF-beta 1 falls into the category of type II, whereas that present in the X-ray crystal structure of TGF-beta 2 is more consistent with a type I turn conformation. This may be of functional significance as studies using TGF-beta chimeras and deletion mutants indicate that this portion of the molecule may be important in receptor binding.

Elucidation of the poly-L-proline binding site in Acanthamoeba profilin I by NMR spectroscopy.

The multifunctional protein profilin is one of the most abundant proteins in the cytoplasm and is thought to regulate actin assembly and the phosphoinositide signaling pathway. Profilin binds to several different ligands including actin, poly-L-proline, and the head groups of polyphosphoinositides. Knowledge of profilin/ligand interactions is important for understanding the physiology of profilin in the cell. As a first step in the characterization of profilin/ligand complexes, we have studied a profilin/poly-L-proline complex in solution using high resolution NMR spectroscopy. Analysis of profilin NOE's and chemical shift data indicates that the protein secondary structure is conserved upon binding to poly-L-proline and that the binding site is located between the N- and C-terminal helices in a region rich in highly conserved aromatic sidechains. This site is adjacent to the proposed binding site for actin. In addition, the rate constant for dissociation of the complex is found to be 1.6 +/- 0.2 x 10(4) s-1.

Three-dimensional solution structure of Acanthamoeba profilin-I.

We have determined a medium resolution three-dimensional solution structure of Acanthamoeba profilin-I by multidimensional nuclear magnetic resonance spectroscopy. This 13-kD actin binding protein consists of a five stranded antiparallel beta sheet flanked by NH2- and COOH-terminal helices on one face and by a third helix and a two stranded beta sheet on the other face. Data from actin-profilin cross-linking experiments and the localization of conserved residues between profilins in different phyla indicate that actin binding occurs on the molecular face occupied by the terminal helices. The other face of the molecule contains the residues that differ between Acanthamoeba profilins-I and II and may be important in determining the difference in polyphosphoinositide binding between these isoforms. This suggests that lipids and actin bind to different faces of the molecule.

Secondary structure and topology of Acanthamoeba profilin I as determined by heteronuclear nuclear magnetic resonance spectroscopy.

The protein profilin binds to both actin and the head groups of poly)phosphoinositide)s and may regulate both actin assembly and the phosphoinositide signaling pathway. As a first step in understanding the activity of profilin at the molecular level, we have determined the secondary structure of Acanthamoeba profilin I in solution using multidimensional, heteronuclear NMR spectroscopy. Using a combination of triple-resonance (1H, 13C, 15N) experiments, we obtained virtually complete backbone and side-chain resonance assignments based solely on scalar couplings. 3D and 4D NOESY experiments were then used to determine the secondary structure and global fold of Acanthamoeba profilin I. The central feature of the protein structure is a five-stranded antiparallel beta-sheet flanked by three helices and a short two-stranded antiparallel beta-sheet.

Transforming growth factor beta 1: NMR signal assignments of the recombinant protein expressed and isotopically enriched using Chinese hamster ovary cells.

The transforming growth factor beta s are a homologous family of multifunctional cytokines that regulate cell growth and differentiation. As a prelude to studies of the solution structure and dynamics of TGF-beta 1, we report virtually complete assignment of 1H and 15N resonances for this 25-kDa homodimeric protein. Recombinant TGF-beta 1 was expressed in Chinese hamster ovary cells. The cells were grown either in a completely 15N-enriched medium or in a medium containing selectively 13C, 15N-labeled amino acids to obtain either uniformly or specifically labeled protein, respectively. Two- and three-dimensional heteronuclear edited magnetic resonance spectra of the uniformly 15N-labeled protein and three samples selectively labeled with 13C and 15N yielded assignments for 96% of the backbone amide and C alpha protons and 87% of the side chain protons. To our knowledge, this is the first report of the use of an animal cell expression system to obtain extensive isotopic enrichment in order to sequentially assign a protein. The methodology described herein for the isotopic enrichment and resonance assignments of TGF-beta 1 should be generally applicable to other eukaryotic proteins expressed by animal cells.

Transforming growth factor beta 1: secondary structure as determined by heteronuclear magnetic resonance spectroscopy.

Virtually complete backbone NMR signal assignments have been reported for transforming growth factor beta 1 (TGF-beta 1) [Archer et al. (1993) Biochemistry (preceding paper in this issue)]. Herein we report the secondary structure of the protein in solution on the basis of these assignments and proton NOE's observed in a variety of 2D and 3D heteronuclear NMR spectra. Regular elements of secondary structure derived from the NOE data consist of (a) three helices spanning residues Y58-H68, F24-G29, and N5-F8 and (b) several pairs of two-stranded antiparallel beta-sheets. The longest two-stranded sheet runs from residue L83 to V106 with a type II reverse turn at G93-R94 and a chain twist at residue N103-M104. These elements of regular structure were confirmed by hydrogen exchange, chemical shift, and coupling constant data. With the exception of residues G46-S53, which exhibit relatively few and weak intraresidue NOE's, residues in the rest of the protein adopt an irregular but well-defined structure. All peptide bonds are trans except for a cis peptide bond between Glu35 and Pro36. The structural characteristics observed for TGF-beta 1 in solution generally agree closely with the recently derived crystal structures of TGF-beta 2 [Daopin et al. (1992) Science 257, 369-374; Schlunegger & Grütter (1992) Nature 358, 430-434]. Several noteworthy differences were observed that may be related to function.

Voltage-dependent conductance for alamethicin in phospholipid vesicles. A test for the mechanism of gating.

The ion currents induced by alamethicin were investigated in unilamellar vesicles using electron paramagnetic resonance probe techniques. The peptide induced currents were examined as a function of the membrane bound peptide concentration, and as a function of the transmembrane electrical potential. Because of the favorable partitioning of alamethicin to membranes and the large membrane area to aqueous volume in vesicle suspensions, these measurements could be carried out under conditions where all the alamethicin was membrane bound. Over the concentration range examined, the peptide induced conductances increased approximately with the fourth power of the membrane bound peptide concentration, indicating a channel molecularity of four. When the alamethicin induced currents were examined as a function of voltage, they exhibited a superlinear behavior similar to that seen in planar bilayers. Evidence for the voltage-dependent conduction of alamethicin was also observed in the time dependence of vesicle depolarization. These observations indicate that the voltage-dependent behavior of alamethicin can occur in the absence of a voltage-dependent phase partitioning. That is, a voltage-dependent conformational rearrangement for membrane bound alamethicin leads to a voltage-dependent activity.

Dynamics and aggregation of the peptide ion channel alamethicin. Measurements using spin-labeled peptides.

Two spin-labeled derivatives of the ion conductive peptide alamethicin were synthesized and used to examine its binding and state of aggregation. One derivative was spin labeled at the C-terminus and the other, a leucine analogue, was spin labeled at the N-terminus. In methanol, both the C and N terminal labeled peptides were monomeric. In aqueous solution, the C-terminal derivative was monomeric at low concentrations, but aggregated at higher concentrations with a critical concentration of 23 microM. In the membrane, the C-terminal label was localized to the membrane-aqueous interface using 13C-NMR, and could assume more than one orientation. The membrane binding of the C-terminal derivative was examined using EPR, and it exhibited a cooperativity seen previously for native alamethicin. However, this cooperativity was not the result of an aggregation of the peptide in the membrane. When the spectra of either the C or N-terminal labeled peptide were examined over a wide range of membrane lipid to peptide ratios, no evidence for aggregation could be found and the peptides remained monomeric under all conditions examined. Because electrical measurements on this peptide provide strong evidence for an ion-conductive aggregate, the ion-conductive form of alamethicin likely represents a minor fraction of the total membrane bound peptide.

Localizing the nitroxide group of fatty acid and voltage-sensitive spin-labels in phospholipid bilayers.

The intramembrane locations of several spin labeled probes in small egg phosphatidylcholine (egg PC) vesicles were determined from the enhancement of the 13C nuclear spin lattice relaxation of the membrane phospholipid. Electron paramagnetic resonance (EPR) spectroscopy was also used to measure the relative environmental polarities of the spin labels in egg PC vesicles, ethanol and aqueous solution. The binding location of the spin label group was determined for a pair of hydrophobic ion spin labels, a pair of long chain amphiphiles, and three stearates containing doxyl groups at the 5, 10 and 16 positions. The nuclear relaxation results indicate that the spin label groups on the stearates are located nearer to the membrane exterior than the analogous positions of the unlabeled phospholipid acyl chains. In addition, the spin label groups of the hydrophobic ions and long chain amphiphiles are located near the acyl chain methylene immediately adjacent to the carboxyl group. The relative polarities, determined by the EPR technique, are consistent with the nuclear relaxation results. This information, when combined with information on their electrical properties, allows for an assessment of the conformation and position of these voltage sensitive probes in membranes.

Localization of hydrophobic ions in phospholipid bilayers using 1H nuclear Overhauser effect spectroscopy.

The binding location for the hydrophobic ions tetraphenylphosphonium (TPP+) and tetraphenylboron (TPB-) was studied in sonicated phosphatidylcholine (PC) vesicles by measuring time-dependent and steady-state intermolecular 1H nuclear Overhauser effects (NOE's). Intermolecular cross-relaxation was also investigated by two-dimensional NOE spectroscopy. Information on the distance and order parameter dependence of the NOE's was obtained from a simple simulation of the NOE's in the alkyl chain region. Taken together, the NOE data and the simulation provide strong evidence that TPB- and TPP+, at low concentrations (less than or equal to 10 mol%), are localized in the alkyl chain region of the bilayer. At these lower concentrations of TPP+ or TPB-, no significant effect on lipid 13C T1 or T2 relaxation rates is detected. The proposed location is consistent with the expected free energy profiles for hydrophobic ions and with the carbonyl oxygens or interfacial water as the source of the membrane dipole potential. At higher ion/lipid ratios (greater than or equal to 20 mol%), TPB-/lipid NOE's increase. This results from a specific association of TPB- with the choline head group.

Birth order and intelligence: an immunological interpretation.

The literature indicates that the IQs and school performance of children tend to decline with increasing order of birth. A hypothesis is here presented that the effect of birth order upon intellectual performance may result from an increasing probability of maternal immune attack upon the fetal brain in utero with order of parity. In support of this hypothesis, evidence is adduced from the literature that the fetal brain is antigenic, that fetal antigens may reach the immune system of the mother, that the incidence of maternal sensitization to fetal antigens increases with parity, that antibodies may readily cross the placenta and reach the fetal brain, that antibodies can be highly teratogenic, and that certain antibodies may damage, in a lasting way, the structure, function, and learning capacity of brains in experimental animals and human infants.

Extraction and identification of a human pancreatic-tumor-associated antigen.

In attempting to develop an immunoassay to aid in the early diagnosis of cancer of the pancreas, a pancreatic-tumor-associated antigen (TAA) was identified and partially purified. The antigen has a molecular weight of approximately 380,000, does not cross-react with carcinoembryonic antigen (CEA), and is apparently either not present or not readily detectable in normal pancreatic tissue. The development of an immunoassay employing such an antigen to aid in the diagnosis of cancer of the pancreas at an early stage of development is discussed.

Isolation and characterization of a rabbit T lymphocyte-specific antigen.

Rabbit T lymphocytes may be differentiated from B lymphocytes by the presence of a T lymphocyte-specific surface antigen. This unique antigen has been extracted from the plasma membrane of rabbit thymocytes by 3 M KCl. The presence of the antigen in the membrane extract was demonstrated by inhibition of cytotoxicity with goat anti-rabbit T cell serum (ATS). The crude membrane extract was fractionated by gel electrophoresis and the fractions containing the T cell antigen identified by inhibition of cytotoxic ATS and by passive hemagglutination. The purified T cell antigen was found to have a m.w. of approximately 12,000 and contained approximately 2.5% carbohydrate. Evidence was also obtained to suggest that the rabbit T cell antigen exists in multiple forms, each having the same m.w. but exhibiting different electrophoretic characteristics.

Induction of a T-cell specific antigen on bone marrow lymphocytes with thymus RNA.

Expression of a rabbit T-cell specific antigen can be induced on bone marrow lymphocytes following exposure to an RNA extract obtained from the thymuses of young rabbits. The presence of the antigen was demonstrated using goat anti-rabbit T-cell serum in a complement-dependent cytotoxicity assay. The T-cell antigen first appeared 3 h after addition of the thymus RNA to bone marrow cell cultures and the maximum number of cells expressing the T-cell antigen was observed within 24 h. RNA obtained from a source other than the thymus was found to be ineffective in inducing expression of the T-cell antigen. The induction of the antigen appears to be dependent on the presence of intact thymus RNA, as RNase treatment but not trypsin treatment, destroyed the ability of the RNA to induce the T-cell antigen.