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Biomedical subjects

A Sali

Publications and source records attributed to A Sali.

At least 55 records · Page 3Linked to original sources
PubMed2000

Comparative protein structure modeling of genes and genomes.

Comparative modeling predicts the three-dimensional structure of a given protein sequence (target) based primarily on its alignment to one or more proteins of known structure (templates). The prediction process consists of fold assignment, target-template alignment, model building, and model evaluation. The number of protein sequences that can be modeled and the accuracy of the predictions are increasing steadily because of the growth in the number of known protein structures and because of the improvements in the modeling software. Further advances are necessary in recognizing weak sequence-structure similarities, aligning sequences with structures, modeling of rigid body shifts, distortions, loops and side chains, as well as detecting errors in a model. Despite these problems, it is currently possible to model with useful accuracy significant parts of approximately one third of all known protein sequences. The use of individual comparative models in biology is already rewarding and increasingly widespread. A major new challenge for comparative modeling is the integration of it with the torrents of data from genome sequencing projects as well as from functional and structural genomics. In particular, there is a need to develop an automated, rapid, robust, sensitive, and accurate comparative modeling pipeline applicable to whole genomes. Such large-scale modeling is likely to encourage new kinds of applications for the many resulting models, based on their large number and completeness at the level of the family, organism, or functional network.

Animals↗
PubMed1999

Identification of a new member of the tryptase family of mouse and human mast cell proteases which possesses a novel COOH-terminal hydrophobic extension.

Mapping of the tryptase locus on chromosome 17 revealed a novel gene 2.3 kilobase 3' of the mouse mast cell protease (mMCP) 6 gene. This 3.7-kilobase gene encodes the first example of a protease in the tryptase family that contains a membrane-spanning segment located at its COOH terminus. Comparative structural studies indicated that the putative transmembrane tryptase (TMT) possesses a unique substrate-binding cleft. As assessed by RNA blot analyses, mTMT is expressed in mice in both strain- and tissue-dependent manners. Thus, different transcriptional and/or post-transcriptional mechanisms are used to control the expression of mTMT in vivo. Analysis of the corresponding tryptase locus in the human genome resulted in the isolation and characterization of the hTMT gene. The hTMT transcript is expressed in numerous tissues and is also translated. Analysis of the tryptase family of genes in mice and humans now indicates that a primordial serine protease gene duplicated early and often during the evolution of mammals to generate a panel of homologous tryptases in each species that differ in their tissue expression, substrate specificities, and physical properties.

Amino Acid Sequence↗
PubMed1999

Convergent evolution of Trichomonas vaginalis lactate dehydrogenase from malate dehydrogenase.

Lactate dehydrogenase (LDH) is present in the amitochondriate parasitic protist Trichomonas vaginalis and some but not all other trichomonad species. The derived amino acid sequence of T. vaginalis LDH (TvLDH) was found to be more closely related to the cytosolic malate dehydrogenase (MDH) of the same species than to any other LDH. A key difference between the two T. vaginalis sequences was that Arg91 of MDH, known to be important in coordinating the C-4 carboxyl of oxalacetate/malate, was replaced by Leu91 in LDH. The change Leu91Arg by site-directed mutagenesis converted TvLDH into an MDH. The reverse single amino acid change Arg91Leu in TvMDH, however, gave a product with no measurable LDH activity. Phylogenetic reconstructions indicate that TvLDH arose from an MDH relatively recently.

Amino Acid Sequence↗
PubMed1999

Differential mechanisms of inorganic pyrophosphate production by plasma cell membrane glycoprotein-1 and B10 in chondrocytes.

OBJECTIVE: Increased nucleoside triphosphate pyrophosphohydrolase (NTPPPH) activity in chondrocytes is associated with cartilage matrix inorganic pyrophosphate (PPi) supersaturation in chondrocalcinosis. This study compared the roles of the transforming growth factor beta (TGFbeta)-inducible plasma cell membrane glycoprotein-1 (PC-1) and the closely related B10 NTPPPH activities in chondrocyte PPi metabolism. METHODS: NTPPPH expression was studied using reverse transcriptase-polymerase chain reaction and Western blotting. Transmembrane PC-1 (tmPC-1), water-soluble secretory PC-1 (secPC-1), and transmembrane B10 were expressed by adenoviral gene transfer or plasmid transfection, and expression of PPi was assessed in cultured articular chondrocytes and immortalized NTPPPH-deficient costal chondrocytes (TC28 cells). RESULTS: PC-1 and B10 messenger RNA were demonstrated in articular cartilages in situ, in untreated cultured normal articular chondrocytes, and in TC28 cells. Expression of tmPC-1 and secPC-1, but not B10, rendered the NTPPPH-deficient TC28 cells able to increase expression of extracellular PPi, with or without addition of TGFbeta (10 ng/ml) to the media. More plasma membrane NTPPPH activity was detected in cells transfected with tmPC-1 than in cells transfected with B10. Furthermore, confocal microscopy with immunofluorescent staining of articular chondrocytes confirmed preferential plasma membrane localization of PC-1, relative to B10. Finally, both PC-1 and B10 increased the levels of intracellular PPi, but PC-1 and B10 appeared to act principally in different intracellular compartments (Golgi and post-Golgi versus pre-Golgi, respectively). CONCLUSION: PC-1 and B10 NTPPPH activities were not redundant in chondrocytes. Although increased PC-1 and B10 expression caused elevations in intracellular PPi, the major effects of PC-1 and B10 were exerted in distinct subcellular compartments. Moreover, PC-1 (transmembrane and secreted), but not B10, increased the levels of extracellular PPi. Differential expression of PC-1 and B10 could modulate cartilage mineralization in degenerative joint diseases.

Brefeldin A↗
PubMed1999

lynx1, an endogenous toxin-like modulator of nicotinic acetylcholine receptors in the mammalian CNS.

Elapid snake venom neurotoxins exert their effects through high-affinity interactions with specific neurotransmitter receptors. A novel murine gene, lynx1, is highly expressed in the brain and contains the cysteine-rich motif characteristic of this class of neurotoxins. Primary sequence and gene structure analyses reveal an evolutionary relationship between lynx1 and the Ly-6/neurotoxin gene family. lynx1 is expressed in large projection neurons in the hippocampus, cortex, and cerebellum. In cerebellar neurons, lynx1 protein is localized to a specific subdomain including the soma and proximal dendrites. lynx1 binding to brain sections correlates with the distribution of nAChRs, and application of lynx1 to Xenopus oocytes expressing nAChRs results in an increase in acetylcholine-evoked macroscopic currents. These results identify lynx1 as a novel protein modulator for nAChRs in vitro, which could have important implications in the regulation of cholinergic function in vivo.

Adaptor Proteins, Signal Transducing↗
PubMed1999

Immunoglobulin motif DNA recognition and heterodimerization of the PEBP2/CBF Runt domain.

The polyomavirus enhancer binding protein 2 (PEBP2) or core binding factor (CBF) is a heterodimeric enhancer binding protein that is associated with genetic regulation of hematopoiesis and osteogenesis. Aberrant forms of PEBP2/CBF are implicated in the cause of the acute human leukemias and in a disorder of bone development known as cleidocranial dysplasia. The common denominator in the natural and mutant forms of this protein is a highly conserved domain of PEBP2/CBF alpha, termed the Runt domain (RD), which is responsible for both DNA binding and heterodimerization with the beta subunit of PEBP2/CBF. The three-dimensional structure of the RD bound to DNA has been determined to be an S-type immunoglobulin fold, establishing a structural relationship between the RD and the core DNA binding domains of NF-kappaB, NFAT1, p53 and the STAT proteins. NMR spectroscopy of a 43.6 kD RD-beta-DNA ternary complex identified the surface of the RD in contact with the beta subunit, suggesting a mechanism for the enhancement of RD DNA binding by beta. Analysis of leukemogenic mutants within the RD provides molecular insights into the role of this factor in leukemogenesis and cleidocranial dysplasia.

Cleidocranial Dysplasia↗
PubMed1999

Structural genomics: beyond the human genome project.

With access to whole genome sequences for various organisms and imminent completion of the Human Genome Project, the entire process of discovery in molecular and cellular biology is poised to change. Massively parallel measurement strategies promise to revolutionize how we study and ultimately understand the complex biochemical circuitry responsible for controlling normal development, physiologic homeostasis and disease processes. This information explosion is also providing the foundation for an important new initiative in structural biology. We are about to embark on a program of high-throughput X-ray crystallography aimed at developing a comprehensive mechanistic understanding of normal and abnormal human and microbial physiology at the molecular level. We present the rationale for creation of a structural genomics initiative, recount the efforts of ongoing structural genomics pilot studies, and detail the lofty goals, technical challenges and pitfalls facing structural biologists.

Computational Biology↗
PubMed1999

Outcome analyses in 1072 surgically treated lumbar disc herniations.

This article reports the outcomes of 1072 consecutive patients surgically treated during a ten-year period. There are many new techniques for the treatment for lumbar disc hernia, but also the conventional standard discectomy procedure is still the most acceptable method today. 1072 consecutive, non-randomized patients with lumbar disc herniation were reviewed for a clinical retrospective study about the surgical outcome according to our functional grading system. The patients reported ruptured disc to be due to lifting (30.13%), trauma (9.42%), and sports (8.11%). Almost all patients had complained of radicular pain in a dermatomal distribution (90.39%) and 86.07% had low-back pain, 5.2% of the patients had complications. Eighty-five patients (7.92%) had a second lumbar disc operation. Thirty of these eighty-five patients underwent the operation at the same level. Patients were also rated to improve the ability. Almost 91% of the patients had excellent, good, and satisfactory outcome; 9% of patients had moderate and poor categories of outcome. Several conclusions can be drawn from this large series of patients who were operated for lumbar disc herniation. 1. Most patients had good-to-excellent surgical outcomes after lumbar discectomy. 2. The results of disc surgery depend not only upon operative technique and skill, the degree of neurological impairment but also upon the correct selection of cases.

Adolescent↗
PubMed1999

Challenges at the frontiers of structural biology.

Knowledge of the three-dimensional structures of proteins is the key to unlocking the full potential of genomic information. There are two distinct directions along which cutting-edge research in structural biology is currently moving towards this goal. On the one hand, tightly focused long-term research in individual laboratories is leading to the determination of the structures of macromolecular assemblies of ever-increasing size and complexity. On the other hand, large consortia of structural biologists, inspired by the pace of genome sequencing, are developing strategies to determine new protein structures rapidly, so that it will soon be possible to predict reasonably accurate structures for most protein domains. We anticipate that a small number of complex systems, studied in depth, will provide insights across the field of biology with the aid of genome-based comparative structural analysis.

Animals↗
PubMed1998

Large-scale protein structure modeling of the Saccharomyces cerevisiae genome.

The function of a protein generally is determined by its three-dimensional (3D) structure. Thus, it would be useful to know the 3D structure of the thousands of protein sequences that are emerging from the many genome projects. To this end, fold assignment, comparative protein structure modeling, and model evaluation were automated completely. As an illustration, the method was applied to the proteins in the Saccharomyces cerevisiae (baker's yeast) genome. It resulted in all-atom 3D models for substantial segments of 1,071 (17%) of the yeast proteins, only 40 of which have had their 3D structure determined experimentally. Of the 1,071 modeled yeast proteins, 236 were related clearly to a protein of known structure for the first time; 41 of these previously have not been characterized at all.

Fungal Proteins↗
PubMed1998

Crystal structure of a GCN5-related N-acetyltransferase: Serratia marcescens aminoglycoside 3-N-acetyltransferase.

The X-ray structure of a canonical GCN5-related N-acetyltransferase (GNAT), Serratia marcescens aminoglycoside 3-N-acetyltransferase, bound to coenzyme A (CoA) has been determined at 2.3 A resolution. The single domain alpha/beta protein resembles a cupped right hand wrapped around a cylinder and consists of a highly curved, six-stranded beta sheet of mixed polarity that is sandwiched between four alpha helices. The structure includes all four conserved GNAT motifs (C, D, A, and B) and represents the catalytic core of this large enzyme superfamily. Acetyl CoA recognition is mediated by a betaalpha structure derived from GNAT motif A, which presents an invariant Arg/Gln-X-X-Gly-X-Gly/Ala segment for hydrogen bonding with the cofactor. Motif B contributes acidic residues to the binding site for the positively charged antibiotic substrate.

Acetyltransferases↗
PubMed1998

Current insights into the "antiphospholipid" syndrome: clinical, immunological, and molecular aspects.

Advances in defining the target antigen(s) for the autoantibodies in the APS highlight the inadequacies of the current classification of these autoantibodies into anticardiolipin and LA antibodies. The discovery that beta 2GPI is the target antigen for the autoantibodies detected in solid-phase immunoassays has opened a number of areas of research linking these autoantibodies to atherogenesis and thrombus formation. Although the role of beta 2GPI in the regulation of blood coagulation in unclear, current evidence suggests that anti-beta 2GPI antibodies interfere with its "normal" role and appear to promote a procoagulant tendency. The expansion of research in this area and the diversity of the clinical manifestations of patients with APS have resulted in the inclusion of molecular biologists and pharmaceutical companies joining immunologists, hematologists, rheumatologists, obstetricians, neurologists, vascular surgeons, and protein and lipid biochemists in attempting to understand the pathophysiology of this condition. Although the published literature may result in conflicting results and introduce new controversies, developing standardized laboratory methods and extrapolation of in vitro experimental results to the vivo situation will advance our understanding of the regulation of the immune system and its interaction with normal hemostatic mechanisms. Since the authors' last review in 1991, the study and understanding of the pathophysiology of APS have evolved from lipid biochemistry to molecular techniques that may eventually provide specific therapies for the clinical manifestations of this condition. Although current treatment has improved the morbidity associated with this condition, especially in improving pregnancy outcomes, future therapies, as outlined in this review, may specifically address the biological abnormalities and have fewer side effects. Better diagnostic tools, such as magnetic resonance imaging with perfusion studies, will allow the study of the true incidence and prevalence of vascular flow changes/tissue ischemia and infarction associated with aPL antibodies and help determine treatment and prophylaxis for APS patients. APS is still the only hypercoagulable condition where both arterial and venous beds can be affected independently or in the same individual.

Antibodies, Antiphospholipid↗
PubMed1998

100,000 protein structures for the biologist.

Structural genomics promises to deliver experimentally determined three-dimensional structures for many thousands of protein domains. These domains will be carefully selected, so that the methods of fold assignment and comparative protein structure modeling will result in useful models for most other protein sequences. The impact on biology will be dramatic.

Animals↗