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PubMed1997

Purine nucleoside phosphorylase. 2. Catalytic mechanism.

X-ray crystallography, molecular modeling, and site-directed mutagenesis were used to delineate the catalytic mechanism of purine nucleoside phosphorylase (PNP). PNP catalyzes the reversible phosphorolysis of purine nucleosides to the corresponding purine base and ribose 1-phosphate using a substrate-assisted catalytic mechanism. The proposed transition state (TS) features an oxocarbenium ion that is stabilized by the cosubstrate phosphate dianion which itself functions as part of a catalytic triad (Glu89-His86-PO4=). Participation of phosphate in the TS accounts for the poor hydrolytic activity of PNP and is likely to be the mechanistic feature that differentiates phosphorylases from glycosidases. The proposed PNP TS also entails a hydrogen bond between N7 and a highly conserved Asn. Hydrogen bond donation to N7 in the TS stabilizes the negative charge that accumulates on the purine ring during glycosidic bond cleavage. Kinetic studies using N7-modified analogs provided additional support for the hydrogen bond. Crystallographic studies of 13 human PNP-ligand complexes indicated that PNP uses a ligand-induced conformational change to position Asn243 and other key residues in the active site for catalysis. These studies also indicated that purine nucleosides bind to PNP with a nonstandard glycosidic torsion angle (+anticlinal) and an uncommon sugar pucker (C4'-endo). Single point energy calculations predicted the binding conformation to enhance phosphorolysis through ligand strain. Structural data also suggested that purine binding precedes ribose 1-phosphate binding in the synthetic direction whereas the order of substrate binding was less clear for phosphorolysis. Conservation of the catalytically important residues across nucleoside phosphorylases with specificity for 6-oxopurine nucleosides provided further support for the proposed catalytic mechanism.

Amino Acid Sequence↗

PubMed2005

Multilevel microfluidics via single-exposure photolithography.

This communication reports a new method to form multilevel features in a single layer of SU-8 photoresist to facilitate the generation of 3D microfluidic chips. The method utilizes the spatial dependence of diffracted light intensity to selectively overexpose masked regions of photoresist and requires only a UV light source and a single transparency mask. 3D structures are formed within microfluidic channels using this selective overexposure method, with feature sizes being determined by the exposure dose and mask feature sizes. The dimensions of the internal features and the microfluidic channels can be varied independently according to these parameters, and any number of different heights can be obtained in a single exposure step. The method provides a simple means of forming 3D microfluidic structures with integrated features, including mixing structures, flow stabilization ridges, and separation weirs to increase the capabilities of microfluidic chips in a variety of microchemical applications.

Journal Article↗

PubMed2005

Potent androgen antagonists based on carborane as a hydrophobic core structure.

Carboranes (dicarba-closo-dodecaboranes) are a class of carbon-containing polyhedral boron-cluster compounds having remarkable chemical and thermal stability and hydrophobic character. These features may allow application of carboranes as a new hydrophobic core structure in biologically active molecules that interact hydrophobically with receptors. We report here the design and synthesis of novel androgen antagonists bearing carborane. The most potent compounds, the arylcarborane derivatives 6e and 6i, exhibited antiandrogenic activity greater than that of the well-known antiandrogen hydroxyflutamide in reporter gene assay using NIH3T3 cells transfected with a human AR expression plasmid, as well as in cell growth inhibition assay using androgen-dependent SC-3 cells. Further development of the potent carborane-containing androgen antagonists described here, having a new skeletal structure and unique characteristics, may yield novel therapeutic agents, especially selective androgen receptor modulators.

Androgen Antagonists↗

PubMed2004

Generation of amino-terminated surfaces by chemical lithography using atomic force microscopy.

Self-assembled monolayers (SAMs) covered with nitroso end groups were reduced using an atomic force microscope. As the bias voltage become more negative (beyond -4 V), the surface potential of the scanned area become closer to that of the amino-terminated SAM. Following this chemical change, however, no change in topographic features was detected, implying retained stability of the underlying SAM layer. We then released carboxylate-modified polystyrene (PS) spheres into a pH 4 solution containing the sample. Subsequent imaging with atomic force microscopy (AFM) revealed that these PS spheres were only selectively immobilized on the regions that were originally scanned at -6 V to form amino termination. In summary, using AFM set to a specific voltage, we were able to selectively generate micropatterned regions of the SAM with amino termination.

Amines↗

PubMed1997

Identification of parvalbumin alpha in bovine hypothalamus: a partial primary structure.

In the course of the study of structure-functional properties and molecular mechanisms of neuropeptides and of low molecular weight proteins of the central nervous system we succeeded in isolating from the soluble fraction of bovine hypothalamus a protein having M(r) 11897.3, according to mass spectral analysis. The purification procedure was mainly based on reversed phase HPLC. As the N-terminus of the molecule was found to be blocked, we have subjected it to CNBr degradation. By Edman microsequence analysis of the peptide fragments and by data base searching the isolated substance was identified as parvalbumin alpha (PRVA)-one of the calcium-binding proteins. However, its primary structure was found not to be identical to that of the known PRVAs from other sources. One of the features of PRVA is its stability. Being subjected to an exhausting purification procedure it retains its complete structure. As neuropeptides and low molecular weight proteins are found to be polyfunctional, a central question concerns the biological role of PRVAs in terms of "where and when" they express their action.

Amino Acid Sequence↗

PubMed1984

The solution structure of a RNA pentadecamer comprising the anticodon loop and stem of yeast tRNAPhe. A 500 MHz 1H-n.m.r. study.

A 500 MHz 1H-n.m.r. study on the semi-synthetic RNA pentadecamer 5'-r(C-A-G-A-Cm-U-Gm-A-A-Y-A-psi-m5C-U-G) comprising the anticodon loop and stem (residues 28-42) of yeast tRNAPhe is presented. By using pre-steady-state nuclear-Overhauser-effect measurements all exchangeable and non-exchangeable base proton resonances, all H1' ribose resonances and all methyl proton resonances are assigned and over 70 intra- and inter-nucleotide interproton distances determined. From the distance data the solution structure of the pentadecamer is solved by model-building. It is shown that the pentadecamer adopts a hairpin-loop structure in solution with the loop in a 3'-stacked conformation. This structure is both qualitatively and quantitatively remarkably similar to that of the anticodon loop and stem found in the crystal structures of tRNAPhe with an overall root-mean-square difference of 0.12 nm between the interproton distances determined by n.m.r. and X-ray crystallography. The hairpin-loop solution structure of the pentadecamer is very stable with a 'melting' temperature of 53 degrees C in 500 mM-KCl, and the structural features responsible for this high stability are discussed. Interaction of the pentadecamer with the ribotrinucleoside diphosphate UpUpC, one of the codons for the amino acid phenylalanine, results only in minor perturbations in the structure of the pentadecamer, and the 3'-stacked conformation of the loop is preserved. The stability of the pentadecamer-UpUpC complex (K approximately 2.5 X 10(4) M-1 at 0 degrees C) is approximately an order of magnitude greater than that of the tRNAPhe-UpUpC complex.

Anticodon↗

PubMed2000

The riboflavin/FAD cycle in rat liver mitochondria.

Here we provide evidence that mitochondria isolated from rat liver can synthesize FAD from riboflavin that has been taken up and from endogenous ATP. Riboflavin uptake takes place via a carrier-mediated process, as shown by the inverse relationship between fold accumulation and riboflavin concentration, the saturation kinetics [riboflavin Km and Vmax values were 4.4+/-1.3 microM and 35+/-5 pmol x min(-1) (mg protein)(-1), respectively] and the inhibition shown by the thiol reagent mersalyl, which cannot enter the mitochondria. FAD synthesis is due to the existence of FAD synthetase (EC 2.7.7.2), localized in the matrix, which has as a substrate pair mitochondrial ATP and FMN synthesized from taken up riboflavin via the putative mitochondrial riboflavin kinase. In the light of certain features, including the protein thermal stability and molecular mass, mitochondrial FAD synthetase differs from the cytosolic isoenzyme. Apparent Km and apparent Vmax values for FMN were 5.4+/-0.9 microM and 22.9+/-1.4 pmol x min(-1) x (mg matrix protein)(-1), respectively. Newly synthesized FAD inside the mitochondria can be exported from the mitochondria in a manner sensitive to atractyloside but insensitive to mersalyl. The occurrence of the riboflavin/FAD cycle is proposed to account for riboflavin uptake in mitochondria biogenesis and riboflavin recovery in mitochondrial flavoprotein degradation; both are prerequisites for the synthesis of mitochondrial flavin cofactors.

Animals↗

PubMed1999

First worldwide clinical experience with a new dual chamber implantable cardioverter defibrillator. Advantages and complications. The Ventak AV II DR investigators.

AIMS: The need for physiological pacing and for improving the ability to discriminate atrial from ventricular tachyarrhythmias has prompted the development of dual chamber implantable cardioverter/defibrillators (ICDs). METHODS: Fifty-two patients were implanted with a newly developed dual-chamber ICD providing rate-responsive physiological pacing (Ventak AV II DR). The device possesses two new arrhythmia detection algorithms ('atrial fibrillation rate threshold' and 'ventricular to atrial rate relationship') in addition to commonly used features such as 'onset' and 'stability'. During implantation, the atrial and ventricular lead impedances and pacing thresholds were determined together with the defibrillation threshold. Prior to discharge, attempts were made to induce both atrial and ventricular tachyarrhythmias in order to test those new detection criteria. All patients were followed for at least 3 months. RESULTS: The device was successfully implanted in all 52 patients. Placement of the atrial lead was successful in 50/52 patients (96%; P-wave 3.2 +/- 1.4 mV; impedance 576 +/- 123 omega; atrial pacing threshold 1.2 +/- 0.9 V). Prior to discharge, 32 episodes of atrial fibrillation (AF) alone, 38 episodes of AF with ventricular fibrillation and 10 episodes of AF with monomorphic ventricular tachycardia were induced in 33/50 patients (66%) and all were appropriately classified by the detection algorithm. During the 3 months follow-up, 12 patients (23%) had appropriate and successful therapies for ventricular arrhythmias, while four patients (8%) experienced inappropriate ICD therapies. Although all these episodes were detected correctly as supraventricular arrhythmias by the device, therapy was delivered because of incorrect or incomplete programming. In all cases reprogramming of the device resolved the problem. CONCLUSION: Implantation of dual chamber ICDs is feasible and appears to improve discrimination of supraventricular from ventricular tachyarrhythmias. In addition, patients with tachyarrhythmias and concomitant bradyarrhythmias may benefit from simultaneous physiological pacing. However, implantation and follow-up of such patients should be performed at experienced centres since both surgical handling and programming of these devices is more difficult and complex than conventional ICDs.

Algorithms↗

PubMed2000

The Dewar photoproduct of thymidylyl(3'-->5')- thymidine (Dewar product) exhibits mutagenic behavior in accordance with the "A rule".

In contrast to the highly mutagenic pyrimidine(6-4)pyrimidone photoproduct, its Dewar valence isomer (Dewar product) has low mutagenic potential and produces a broad range of mutations [LeClerc, J. E., Borden, A. & Lawrence, C. W. (1991) Proc. Natl. Acad. Sci. USA 88, 9685-9689]. To determine the origin of the mutagenic property of the Dewar product, we used experimental NMR restraints and molecular dynamics to determine the solution structure of a Dewar-lesion DNA decamer duplex. This DNA decamer duplex (DW/GA duplex) contains a mismatched base pair between the 3' T residue of the Dewar lesion (T6) and an opposed G residue (G15). The 3' T (T6) of the Dewar lesion formed stable hydrogen bonds with the opposing G15 residue. However, the helical bending and unwinding angles of the DW/GA duplex were much larger than those of a second duplex that contains the Dewar lesion and opposing A15 and A16 residues (DW/AA duplex). The DW/GA duplex showed poorer stacking interactions at the two bases of the Dewar product and at the adjacent A7 small middle dotT14 base pair than did the DW/AA duplex. These structural features imply that no thermal stability or conformational benefit is obtained by incorporating a G instead of an A opposite the 3' T of the Dewar lesion. These properties may thus facilitate the preferential incorporation of an A in accordance with the A rule during translesion replication and lead to the low frequency of 3' T-->C mutations observed at this site.

Base Sequence↗

PubMed1975

The amphisbaenian ear: Blanus cinereus and Diplometopon zarudnyi.

Observations on the structure and function of the ear in amphisbaenians have been extended to two new species: to Blanus cinereus of the family Amphisbaenidae and Diplometopon zarudnyi of the family Trogonophidae. Blanus, considered one of the most primitive of this group of reptiles, shows a distinctive form of sound-receptive mechanism. The usual extracolumella is lacking, and the columella attaches to a cartilaginous plate beneath the skin posterior to the facial area. Diplometopon zarudnyi, a highly modified trogonophid, shows a columella and extracolumella of massive dimensions, with considerable calcification of the latter process. Cochlear potential measurements revealed the levels of auditory sensitivity in these species. A peculiar feature is the degree of stability of the ear's responses in the presence of large variations in body temperature.

Animals↗

PubMed1998

An autonomous folding unit mediates the assembly of two-stranded coiled coils.

Subunit oligomerization of many proteins is mediated by coiled-coil domains. Although the basic features contributing to the thermodynamic stability of coiled coils are well understood, the mechanistic details of their assembly have not yet been dissected. Here we report a 13-residue sequence pattern that occurs with limited sequence variations in many two-stranded coiled coils and that is absolutely required for the assembly of the Dictyostelium discoideum actin-bundling protein cortexillin I and the yeast transcriptional activator GCN4. The functional relationship between coiled-coil "trigger" sequences was manifested by replacing the intrinsic trigger motif of GCN4 with the related sequence from cortexillin I. We demonstrate that these trigger sequences represent autonomous helical folding units that, in contrast to arbitrarily chosen heptad repeats, can mediate coiled-coil formation. Aside from being of general interest for protein folding, trigger motifs should be of particular importance in the protein de novo design.

Amino Acid Sequence↗

PubMed1998

The variable domain of nonassembled Ig light chains determines both their half-life and binding to the chaperone BiP.

Not much is known about the features that determine the biological stability of a molecule retained in the endoplasmic reticulum (ER). Ig light (L) chains that are not secreted in the absence of Ig heavy (H) chain expression bind to the ER chaperone BiP as partially folded molecules until they are degraded. Although all Ig L chains have the same three-dimensional structure when part of an antibody molecule, the degradation rate of unassembled Ig L chains is not identical. For instance, the two nonsecreted murine Ig L chains, kappaNS1 and lambdaFS62, are degraded with half-lives of approximately 1 and 4 hr, respectively, in the same NS1 myeloma cells. Furthermore, the BiP/lambdaFS62 Ig L chain complex appears to be more stable than the BiP/kappaNS1 complex. Here, we used the ability of single Ig domains to form an internal disulfide bond after folding as a measure of the folding state of kappaNS1 and lambdaFS62 Ig L chains. Both of these nonsecreted L chains lack the internal disulfide bond in the variable (V) domain, whereas the constant (C) domain was folded in that respect. In both cases the unfolded V domain provided the BiP binding site. The stability of BiP binding to these two nonsecreted proteins was quite different, and both the stability of the BiP:Ig L chain complex and the half-life of the Ig L chain could be transferred from one Ig L chain isotype to the other by swapping the V domains. Our data suggest that the physical stability of BiP association with an unfolded region of a given light chain determines the half-life of that light chain, indicating a direct link between chaperone interaction and delivery of partially folded substrates to the mammalian degradation machinery.

Animals↗

PubMed1995

Structure of the metal-free gamma-carboxyglutamic acid-rich membrane binding region of factor IX by two-dimensional NMR spectroscopy.

The gamma-carboxyglutamic acid-rich domain of blood coagulation Factor IX is required for the binding of the protein to phospholipid membranes. To investigate the three-dimensional structure of this domain, a synthetic peptide corresponding to residues 1-47 of Factor IX was studied by 1H NMR spectroscopy. In the absence of metal ions, the proton chemical shift dispersion in the one-dimensional NMR spectrum indicated that the peptide contains regular structural elements. Upon the addition of Ca(II) or Mg(II), large chemical shift changes were observed in the amide proton and methyl proton regions of the spectrum, consistent with the conformational transitions that metal ions are known to induce in native Factor IX. The apopeptide was studied by two-dimensional NMR spectroscopy at 500 MHz to determine its solution structure. Protons were assigned using total correlation spectroscopy, nuclear Overhauser effect spectroscopy, and double quantum-filtered correlation spectroscopy experiments. Intensities of cross-peaks in the nuclear Overhauser effect spectrum were used to generate a set of interproton distance restraints. The structure of the apopeptide was then calculated using distance geometry methods. There are three structural elements in the apopeptide that are linked by a flexible polypeptide backbone. These elements include a short amino-terminal tetrapeptide loop (amino acids 6-9), the disulfide-containing hexapeptide loop (amino acids 18-23), and a carboxyl-terminal alpha helix (amino acids 37-46). Amide hydrogen exchange kinetics indicate that the majority of the peptide is solvent accessible, except in the carboxyl-terminal element. The structured regions in the apopeptide are insufficient to support phospholipid binding, indicating the importance of additional structural features in the Ca(II)-stabilized conformer.

1-Carboxyglutamic Acid↗

PubMed2000

Crystal structure of a thermophilic cytochrome P450 from the archaeon Sulfolobus solfataricus.

The structure of the first P450 identified in Archaea, CYP119 from Sulfolobus solfataricus, has been solved in two different crystal forms that differ by the ligand (imidazole or 4-phenylimidazole) coordinated to the heme iron. A comparison of the two structures reveals an unprecedented rearrangement of the active site to adapt to the different size and shape of ligands bound to the heme iron. These changes involve unraveling of the F helix C-terminal segment to extend a loop structure connecting the F and G helices, allowing the longer loop to dip down into the active site and interact with the smaller imidazole ligand. A comparison of CYP119 with P450cam and P450eryF indicates an extensive clustering of aromatic residues may provide the structural basis for the enhanced thermal stability of CYP119. An additional feature of the 4-phenylimidazole-bound structure is a zinc ion tetrahedrally bound by symmetry-related His and Glu residues.

Archaeal Proteins↗

PubMed2000

HELM: searching for helix motifs within protein sequences.

SUMMARY: HELM is a web tool designed to automate the analysis of protein sequences searching for alpha helix motifs. This analysis can be useful in protein engineering studies, aimed at the identification of regions to be modified in order to obtain more suitable features of local and/or global stability. AVAILABILITY: The tool is available to academic and commercial institutions at the URL http://crisceb.area.na.cnr.it/angelo/ PROTEIN_TOOLS/HELM/ CONTACT: angelo@crisceb.area.na.cnr.it

Amino Acid Motifs↗

PubMed1993

Pulmonary embolus and patent foramen ovale: a rare cause of refractory hypoxaemia.

A patient with a large pulmonary embolus is described. The striking features were those of cardiovascular stability with hypoxaemia and hypercapnia. Cardiac catheterization confirmed the pulmonary embolus; in addition there was found to be a patent foramen ovale (PFO), causing a large right-to-left shunt. Removal of the pulmonary embolus and closure of the PFO dramatically improved alveolar-arterial oxygen gradient and ventilatory requirements.

Heart Septal Defects, Atrial↗

PubMed2001

CKAAPs DB: a conserved key amino acid positions database.

The Conserved Key Amino Acid Positions DataBase (CKAAPs DB) provides access to an analysis of structurally similar proteins with dissimilar sequences where key residues within a common fold are identified. The derivation and significance of CKAAPs starting from pairwise structure alignments is described fully in Reddy et al. [Reddy,B.V.B., Li,W.W., Shindyalov,I.N. and Bourne,P.E. (2000) PROTEINS:, in press]. The CKAAPs identified from this theoretical analysis are provided to experimentalists and theoreticians for potential use in protein engineering and modeling. It has been suggested that CKAAPs may be crucial features for protein folding, structural stability and function. Over 170 substructures, as defined by the Combinatorial Extension (CE) database, which are found in approximately 3000 representative polypeptide chains have been analyzed and are available in the CKAAPs DB. CKAAPs DB also provides CKAAPs of the representative set of proteins derived from the CE and FSSP databases. Thus the database contains over 5000 representative poly-peptide chains, covering all known structures in the PDB. A web interface to a relational database permits fast retrieval of structure-sequence alignments, CKAAPs and associated statistics. Users may query by PDB ID, protein name, function and Enzyme Classification number. Users may also submit protein alignments of their own to obtain CKAAPs. An interface to display CKAAPs on each structure from a web browser is also being implemented. CKAAPs DB is maintained by the San Diego Supercomputer Center and accessible at the URL http://ckaaps.sdsc.edu.

Algorithms↗

PubMed1997

Open reduction and internal fixation with bone grafting of clavicular nonunion.

BACKGROUND: Although clavicular fractures are common, nonunion of the clavicle is a rare complication. However, it can be disabling, presenting mainly with pain, limitation of shoulder movement, and/or compression of the brachial plexus. The technical difficulty in securing adequate skeletal stabilization and the unique anatomic features of the clavicle pose a challenge for the orthopedic surgeon. METHODS: Sixteen patients with symptomatic nonunion of the clavicle were studied. They were nine men and seven women with a median age of 34 years (range, 15-52 years). The average follow-up was 12.9 months (range, 9-24 months). The nonunion was hypertrophic in 11 cases, atrophic in five cases, and showed pseudoarthrosis in one case. The primary indication for performing the operation was pain in all cases. Five of the 16 cases had previous operations. All cases were treated with open reduction and internal fixation using a reconstruction plate or a dynamic compression plate. Double plating was used in three cases. Autogenous bone grafting was applied in 14 cases and corraline hydroxyapatite in one case. RESULTS: Fifteen of the 16 fractures eventually healed with complete resolution of the preoperative pain, except in two cases who had persistent mild pain. The hardware was removed after union in one case. One hardware failure required revision and eventually went on to heal. Another hardware failure required removal because of pain. The pain subsided despite the persistent nonunion. The same patient had hematoma at the site of the bone graft and continued to have pain until the last follow-up. CONCLUSION: Plating and bone grafting of the clavicle is an effective method of management of painful nonunion, and it has minimal complications.

Adolescent↗