AS2TS system for protein structure modeling and analysis.

We present a set of programs and a website designed to facilitate protein structure comparison and protein structure modeling efforts. Our protein structure analysis and comparison services use the LGA (local-global alignment) program to search for regions of local similarity and to evaluate the level of structural similarity between compared protein structures. To facilitate the homology-based protein structure modeling process, our AL2TS service translates given sequence-structure alignment data into the standard Protein Data Bank (PDB) atom records (coordinates). For a given sequence of amino acids, the AS2TS (amino acid sequence to tertiary structure) system calculates (e.g. using PSI-BLAST PDB analysis) a list of the closest proteins from the PDB, and then a set of draft 3D models is automatically created. Web services are available at http://as2ts.llnl.gov/.

The major human abasic endonuclease: formation, consequences and repair of abasic lesions in DNA.

DNA continuously suffers the loss of its constituent bases, and thereby, a loss of potentially vital genetic information. Sites of missing bases--termed abasic or apurinic/apyrimidinic (AP) sites--form spontaneously, through damage-induced hydrolytic base release, or by enzyme-catalyzed removal of modified or mismatched bases during base excision repair (BER). In this review, we discuss the structural and biological consequences of abasic lesions in DNA, as well as the multiple repair pathways for such damage, while emphasizing the mechanistic operation of the multi-functional human abasic endonuclease APE1 (or REF-1) and its potential relationship to disease.

Immunoreactivity of organic mimeotopes of the E2 component of pyruvate dehydrogenase: connecting xenobiotics with primary biliary cirrhosis.

In primary biliary cirrhosis (PBC), the major autoepitope recognized by both T and B cells is the inner lipoyl domain of the E2 component of pyruvate dehydrogenase. To address the hypothesis that PBC is induced by xenobiotic exposure, we took advantage of ab initio quantum chemistry and synthesized the inner lipoyl domain of E2 component of pyruvate dehydrogenase, replacing the lipoic acid moiety with synthetic structures designed to mimic a xenobiotically modified lipoyl hapten, and we quantitated the reactivity of these structures with sera from PBC patients. Interestingly, antimitochondrial Abs from all seropositive patients with PBC, but no controls, reacted against 3 of the 18 organic modified autoepitopes significantly better than to the native domain. By structural analysis, the features that correlated with autoantibody binding included synthetic domain peptides with a halide or methyl halide in the meta or para position containing no strong hydrogen bond accepting groups on the phenyl ring of the lysine substituents, and synthetic domain peptides with a relatively low rotation barrier about the linkage bond. Many chemicals including pharmaceuticals and household detergents have the potential to form such halogenated derivatives as metabolites. These data reflect the first time that an organic compound has been shown to serve as a mimeotope for an autoantigen and further provide evidence for a potential mechanism by which environmental organic compounds may cause PBC.

New insights into the structure of abasic DNA from molecular dynamics simulations.

Abasic (AP) sites constitute a common form of DNA damage, arising from the spontaneous or enzymatic breakage of the N-glycosyl bond and the loss of a nucleotide base. To examine the effects of such damage on DNA structure, especially in the vicinity of the abasic sugar, four 1.5 ns molecular dynamics simulations of double-helical DNA dodecamers with and without a single abasic (tetrahydrofuran, X) lesion in a 5'-d(CXT) context have been performed and analyzed. The results indicate that the abasic site does not maintain a hole or gap in the DNA, but instead perturbs the canonical structure and induces additional flexibility close to the abasic site. In the apurinic simulations (i.e., when a pyrimidine is opposite the AP site), the abasic sugar flipped in and out of the minor groove, and the gap was water filled, except during the occurrence of a novel non-Watson-Crick C-T base pair across the abasic site. The apyrimidinic gap was not penetrated by water until the abasic sugar flipped out and remained extrahelical. Both AP helices showed kinks of 20-30 degrees at the abasic site. The Watson-Crick hydrogen bonds are more transient throughout the DNA double helices containing an abasic site. The abasic sugar displayed an unusually broad range of sugar puckers centered around the northern pucker. The increased motion of the bases and backbone near the abasic site appear to correlate with sequence-dependent helical stability. The data indicate that abasic DNA contorts more easily and in specific ways relative to unmodified DNA, an aspect likely to be important in abasic site recognition and hydrolysis.

Mapping the protein-DNA interface and the metal-binding site of the major human apurinic/apyrimidinic endonuclease.

Apurinic/apyrimidinic (AP) endonuclease Ape1 is a key enzyme in the mammalian base excision repair pathway that corrects AP sites in the genome. Ape1 cleaves the phosphodiester bond immediately 5' to AP sites through a hydrolytic reaction involving a divalent metal co-factor. Here, site-directed mutagenesis, chemical footprinting techniques, and molecular dynamics simulations were employed to gain insights into how Ape1 interacts with its metal cation and AP DNA. It was found that Ape1 binds predominantly to the minor groove of AP DNA, and that residues R156 and Y128 contribute to protein-DNA complex stability. Furthermore, the Ape1-AP DNA footprint does not change along its reaction pathway upon active-site coordination of Mg(2+) or in the presence of DNA polymerase beta (polbeta), an interactive protein partner in AP site repair. The DNA region immediately 5' to the abasic residue was determined to be in close proximity to the Ape1 metal-binding site. Experimental evidence is provided that amino acid residues E96, D70, and D308 of Ape1 are involved in metal coordination. Molecular dynamics simulations, starting from the active site of the Ape1 crystal structure, suggest that D70 and E96 bind directly to the metal, while D308 coordinates the cation through the first hydration shell. These studies define the Ape1-AP DNA interface, determine the effect of polbeta on the Ape1-DNA interaction, and reveal new insights into the Ape1 active site and overall protein dynamics.

Interaction and solvation energies of nonpolar DNA base analogues and their role in polymerase insertion fidelity.

Although DNA polymerase fidelity has been mainly ascribed to Watson-Crick hydrogen bonds, two nonpolar isosteres for thymine (T) and adenine (A)--difluorotoluene (F) and benzimidazole (Z) --effectively mimic their natural counterparts in polymerization experiments with pol I (KF exo-) [JC Morales and ET Kool. Nature Struct Biol, 5, 950-954, 1998]. By ab initio quantum chemical gas phase methods (HF/6-31G* and MP2/6-31G**) and a solvent phase method (CPCM-HF/6-31G**), we find that the A-F interaction energy is 1/3 the A-T interaction energy in the gas phase and unstable in the solvent phase. The F-Z and T-Z interactions are very weak and T-Z is quite unstable in the solvent. Electrostatic solvation energy calculations on F, Z and toluene yield that Z is two times, and F and toluene are five times, less hydrophilic than the natural bases. Of the new "base-pairs" (F-Z, T-Z, and F-A), only F-A formed an A-T-like arrangement in unconstrained optimizations. F-Z and T-Z do not freely form planar arrangements, and constrained optimizations show that large amounts of energy are required to make these pairs fit the exact A-T geometry, suggesting that the polymerase does not require all bases to conform to the exact A-T geometry. We discuss a model for polymerase/nucleotide binding energies and investigate the forces and conformational range involved in the polymerase geometrical selection.

Intravenous amino acids, cholestasis and kwashiorkor.

Kwashiorkor dermatosis has not been reported in children on parenteral nutrition (PN). We report a case of kwashiorkor developing in a partially PN dependent patient with cholestasis, when amino acids were removed from the PN solution in an effort to control the cholestasis. Although the kwashiorkor dermatosis improved within 24 hours after the addition of amino acids (1 g/kg) to the PN solution, the cholestasis worsened.

Elements in abasic site recognition by the major human and Escherichia coli apurinic/apyrimidinic endonucleases.

Sites of base loss in DNA arise spontaneously, are induced by damaging agents or are generated by DNA glycosylases. Repair of these potentially mutagenic or lethal lesions is carried out by apurinic/apyrimidinic (AP) endonucleases. To test current models of AP site recognition, we examined the effects of site-specific DNA structural modifications and an F266A mutation on incision and protein-DNA complex formation by the major human AP endonuclease, Ape. Changing the ring component of the abasic site from a neutral tetrahydrofuran (F) to a positively charged pyrrolidine had only a 4-fold effect on the binding capacity of Ape. A non-polar 4-methylindole base analog opposite F had a <2-fold effect on the incision activity of Ape and the human protein was unable to incise or specifically bind 'bulged' DNA substrates. Mutant Ape F266A protein complexed with F-containing DNA with only a 6-fold reduced affinity relative to wild-type protein. Similar studies are described using Escherichia coli AP endonucleases, exonuclease III and endonuclease IV. The results, in combination with previous findings, indicate that the ring structure of an AP site, the base opposite an AP site, the conformation of AP-DNA prior to protein binding and the F266 residue of Ape are not critical elements in targeted recognition by AP endonucleases.

Theory of heterogeneous relaxation in compartmentalized tissues.

A new model of compartmentalized relaxation--that which occurs for spins (protons) exchanging between compartments of different relaxation rates--is presented. This model generalizes previous ones by allowing spatially dependent relaxation within compartments. Solutions for the diffusion-Bloch equations are found via an efficient numerical technique known as the generalized moment expansion, and they agree well with the solutions to the standard two-site exchange equations (TSEE) for many typical situations. Specific models are developed for liposomes, red blood cells, capillaries, and arteries with respect to applied contrast agents. A parameter derived from tissue characteristics is introduced to predict the nature of the solutions. A new method is proposed for using contrast agents to detect capillaries, which exploits their high surface-to-volume ratio relative to the other elements of the vasculature.

Hydration effects on the duplex stability of phosphoramidate DNA-RNA oligomers.

Recent studies on uniformly modified oligonucleotides containing 3'-NHP(O)(O-)O-5'internucleoside linkages (3'amidate) and alternatively modified oligonucleotides containing 3'-O(O-)(O)PNH-5'internucleoside linkages (5'amidate) have shown that 3'amidate duplexes, formed with DNA or RNA complementary strands, are more stable in water than those of the corresponding phosphodiesters. In contrast, 5'amidates do not form duplexes at all. There is no steric reason that the 5'amidate duplex should not form. We demonstrate that these differences arise from differential solvation of the sugar-phosphate backbones. By molecular dynamics calculations on models of 10mer single-stranded DNA and double-stranded DNA-RNA molecules, both with and without the phosphoramidate backbone modifications, we show that the single-stranded 3'amidate and 5'amidate backbones are equally well solvated, but the 5'amidate backbone is not adequately solvated in an A-form duplex. These results are supported by quantum chemical free energy of solvation calculations which show that the 3'amidate backbone is favored relative to the 5'amidate backbone.

A structural basis for a phosphoramide mustard-induced DNA interstrand cross-link at 5'-d(GAC).

Phosphoramide mustard-induced DNA interstrand cross-links were studied both in vitro and by computer simulation. The local determinants for the formation of phosphoramide mustard-induced DNA interstrand cross-links were defined by using different pairs of synthetic oligonucleotide duplexes, each of which contained a single potentially cross-linkable site. Phosphoramide mustard was found to cross-link dG to dG at a 5'-d(GAC)-3'. The structural basis for the formation of this 1,3 cross-link was studied by molecular dynamics and quantum chemistry. Molecular dynamics indicated that the geometrical proximity of the binding sites also favored a 1,3 dG-to-dG linkage over a 1,2 dG-to-dG linkage in a 5'-d(GCC)-3' sequence. While the enthalpies of 1,2 and 1,3 mustard cross-linked DNA were found to be very close, a 1,3 structure was more flexible and may therefore be in a considerably higher entropic state.

Anterior corneal dystrophy with dyscollagenosis (Reis-Bücklers type?).

Anterior corneal dystrophies involving Bowman's membrane and anterior stroma include several subtypes of uncertain etiology: the Reis-Bückler, Thiel-Behnke, Grayson-Wilbrandt, and "honeycomb" dystrophies. The clinical and pathologic features of these dystrophies overlap to such a degree that they may represent variations of the same entity. Typically, they all present symptoms beginning in childhood, have a dominant pattern of heredity, and manifest painful, recurrent corneal erosions. Some cases have also been interpreted as representing macular and granular dystrophy. In the present report, we describe a pedigree of affected patients whose corneal dystrophy shared many of the clinical and pathologic features of the Reis-Bücklers and allied subtypes but which differ from all in causing visual symptoms late in life and with minimal signs of recurrent erosion. Histopathology revealed a thickening of the anterior stroma by the addition of a partially disorganized and degenerating tissue in which collagen Type III (fetal or repair collagen) is intermixed with the normal (mature) Type I collagen in the entire stroma. This is accompanied by irregular swelling of the basal epithelial cells and hyperplasia of the basement membrane (collagen Type IV, laminin and fibronectin), suggesting an aberrant influence of the epithelium on collagen synthesis.

Theory of paramagnetic contrast agents in liposome systems.

We develop a theoretical description of nuclear spin relaxation mediated by MRI contrast agents and transport processes in liposome systems. Such systems compartmentalize the physical space such that paramagnetic contrast agents, which enhance relaxation, are trapped in some subvolume. Due to diffusive transport across compartmental barriers, i.e., across liposome membranes, nuclear spins in the whole volume exhibit fast relaxation. The description developed is based on the diffusion-Bloch equations for the nuclear magnetization with appropriate boundary and continuity conditions. From this set of equations a new inhomogeneous differential equation for the local relaxation times is derived. For simple geometries of compartmentalized spaces the equation can be solved analytically. A simple formula for average relaxation times in liposome systems is presented. The resulting relaxation times agree well with observations.

Unusual tumor of the iris: a rare initial clinical manifestation of metastatic adenocarcinoma of the tail of the pancreas.

The occurrence of an iris tumor with secondary glaucoma as the initial manifestation of an occult pancreatic carcinoma is a rare clinical entity. The subsequent appearance of a testicular mass due to metastatic pancreatic disease also is rare. The use of new advanced diagnostic techniques, such as radioisotope studies and computerized axial tomography, may reveal occult carcinoma of the tail of the pancreas before the inevitable autopsy.

Mixed lacrimal gland tumor arising from ectopic lacrimal gland tissue in the orbit.

An unusual case of lacrimal gland tumor from ectopic lacrimal gland tissue was presented and discussed. Grossly, the tumor was encapsulated and a distinct entity from the surrounding tissues. There were no connections to the lacimal gland and the tumor histologically appeared to be totally encapsulated even though some areas revealed early invasion. The location of the tumor in the orbit was unique, particularly in lieu of its histology, being located nasally and superiorly. A new and rare addition is now added to the differential diagnosis of unilateral exophthalmos.

The exfoliation syndrome.

A clinical and ultramicroscopic review, including discussion of both scanning and transmission microscopy of the exfoliation syndrome, suggests that the term pseudoexfoliation be replaced by exfoliation syndrome. Involvement of the lens epithelium and, particularly, the pigment epithelium of the iris and the ciliary body epithelium are emphasized as being the likely sources of the exfoliative fibrils. A case of exfoliation syndrome in an eye with an eccentric pupil revealed that the granular material seen on the lens capsule occurs only where the iris is in contact with the lens surface and the process may even involve the central anterior capsule under proper conditions. This finding, together with the evidence of continuing deposits after intracapsular cataract extraction, suggests that the granular material is deposited from the iris and that the material formed by the lens epithelium remains within the lens capsule.

Use of immune serum globulin (human) to reduce mortality in newly imported rhesus monkeys (Macaca mulatta).

Immune serum globulin (human) (ISGH) was administered intramuscularly to approximately 5,600 rhesus monkeys weighing between 1.5 and 3.6 kg. The animals were housed at three separate facilities under differing quarantine conditions. ISGH recipients were grossly healthier, suffered less morbidity and fewer developed antibodies against measles (rubeola) virus. Mortality among ISGH-treated animals was only 20-57% of that in the control animals. No adverse effects were seen from the injection of ISGH into rhesus monkeys, and residual antibodies from the injected material could not be detected 18 and 47 days postinoculation.