Search PubMed⌕ Search

Biomedical subjects

M Sundaram

Publications and source records attributed to M Sundaram.

At least 37 records · Page 2Linked to original sources
PubMed2001

Structural basis of pyrimidine specificity in the MS2 RNA hairpin-coat-protein complex.

We have determined the X-ray structures of six MS2 RNA hairpin-coat-protein complexes having five different substitutions at the hairpin loop base -5. This is a uracil in the wild-type hairpin and contacts the coat protein both by stacking on to a tyrosine side chain and by hydrogen bonding to an asparagine side chain. The RNA consensus sequence derived from coat protein binding studies with natural sequence variants suggested that the -5 base needs to be a pyrimidine for strong binding. The five -5 substituents used in this study were 5-bromouracil, pyrimidin-2-one, 2-thiouracil, adenine, and guanine. The structure of the 5-bromouracil complex was determined to 2.2 A resolution, which is the highest to date for any MS2 RNA-protein complex. All the complexes presented here show very similar conformations, despite variation in affinity in solution. The results suggest that the stacking of the -5 base on to the tyrosine side chain is the most important driving force for complex formation. A number of hydrogen bonds that are present in the wild-type complex are not crucial for binding, as they are missing in one or more of the complexes. The results also reveal the flexibility of this RNA-protein interface, with respect to functional group variation, and may be generally applicable to other RNA-protein complexes.

Adenine↗
PubMed2000

Hypermodified nucleosides in the anticodon of tRNALys stabilize a canonical U-turn structure.

Modified nucleosides in the anticodon domain of Escherichia coli tRNA(Lys) are necessary for high-affinity codon recognition and reading frame maintenance. Human tRNA(Lys,3) is the specific primer for HIV-1 reverse transcriptase and also requires nucleoside modification for proper function. We now present NMR solution structures for the fully modified 17-nucleotide E. coli tRNA(Lys) anticodon stem-loop domain (ASL). NMR data were also collected for several partially modified ASLs, revealing the contributions each modified nucleoside (mnm(5)s(2)U34, t(6)A37, and psi39) makes in transforming the disordered, unmodified tRNA ASL into the highly ordered native structure. The solution structure of the native ASL domain provides insight into longstanding questions regarding both wobble position modification and the nearly ubiquitous t(6)A37 found in tRNAs with an adjacent U at position 36. Native tRNA(Lys) has a U-turn structure similar to the yeast tRNA(Phe) crystal structure, unlike previously proposed "unconventional" anticodon structures characterized by stable interactions between mnm(5)s(2)U-34 and t(6)A-37.

Anticodon↗
PubMed2000

Cleavage of the antithrombin III binding site in heparin by heparinases and its implication in the generation of low molecular weight heparin.

Heparin has been used as a clinical anticoagulant for more than 50 years, making it one of the most effective pharmacological agents known. Much of heparin's activity can be traced to its ability to bind antithrombin III (AT-III). Low molecular weight heparin (LMWH), derived from heparin by its controlled breakdown, maintains much of the antithrombotic activity of heparin without many of the serious side effects. The clinical significance of LMWH has highlighted the need to understand and develop chemical or enzymatic means to generate it. The primary enzymatic tools used for the production of LMWH are the heparinases from Flavobacterium heparinum, specifically heparinases I and II. Using pentasaccharide and hexasaccharide model compounds, we show that heparinases I and II, but not heparinase III, cleave the AT-III binding site, leaving only a partially intact site. Furthermore, we show herein that glucosamine 3-O sulfation at the reducing end of a glycosidic linkage imparts resistance to heparinase I, II, and III cleavage. Finally, we examine the biological and pharmacological consequences of a heparin oligosaccharide that contains only a partial AT-III binding site. We show that such an oligosaccharide lacks some of the functional attributes of heparin- and heparan sulfate-like glycosaminoglycans containing an intact AT-III site.

Antithrombin III↗
PubMed2000

Synthesis and characterization of the native anticodon domain of E. coli TRNA(Lys): simultaneous incorporation of modified nucleosides mnm(5)s(2)U, t(6)A, and pseudouridine using phosphoramidite chemistry.

The anticodon domain of E. coli tRNA(Lys) contains the hypermodified nucleosides mnm(5)s(2)U and t(6)A at positions 34 and 37, respectively, along with a more common psi at position 39. The combination of these three nucleotides represents one of the most extensively modified RNA domains in nature. 2-Cyanoethyl diisopropylphosphoramidites of the hypermodified nucleosides mnm(5)s(2)U and t(6)A were each synthesized with protecting groups suitable for automated RNA oligonucleotide synthesis. The 17 nucleotide anticodon stem-loop of E. coli tRNA(Lys) was then assembled from these synthons using phosphoramidite coupling chemistry. Coupling efficiencies for the two hypermodified nucleosides and for pseudouridine phosphoramidite were all greater than 98%. A mild deprotection scheme was developed to accommodate the highly functionalized RNA. High coupling yields, mild deprotection, and efficient HPLC purification allowed us to obtain 1. 8 mg of purified RNA from a 1 micromol scale RNA synthesis. Our efficient synthetic protocol will allow for biophysical investigation of this rather unique tRNA species wherein nucleoside modification has been shown to play a role in codon-anticodon recognition, tRNA aminoacyl synthetase recognition, and programmed ribosomal frameshifting. The human analogue, tRNA(Lys,3), is the specific tRNA primer for HIV-1 reverse transcriptase and has a similar modification pattern.

Anticodon↗
PubMed2000

Unsuspected metastases presenting as solitary soft tissue lesions: a fourteen-year review.

OBJECTIVE: To describe a series of patients with no known primary malignancy who presented with a solitary unsuspected soft tissue metastasis masquerading as a soft tissue sarcoma, and secondarily to describe the imaging appearance of these lesions. DESIGN: Records of two academic hospitals with active orthopedic oncology services were reviewed for patients meeting the above criteria. Clinical charts were examined, and the imaging appearance of the soft tissue lesions retrospectively reviewed. PATIENTS: Of 1421 patients examined for soft tissue lesions, 11 were found who met the above criteria. RESULTS: Of the 11 patients whose initial presentation was a solitary soft tissue metastasis, eight were found to have a primary lung cancer, two were diagnosed with adenocarcinoma of unknown primary, and adenocarcinoma of the colon was discovered in the remaining patient. CONCLUSIONS: The clinical presentation of a solitary soft tissue metastasis without a known primary malignancy is a rare occurrence, with an incidence of approximately 0.8%. Lung cancer is the primary neoplasm in a high percentage of these cases.

Adenocarcinoma↗
PubMed2000

Prospective blinded trial of a fecal antigen test for the detection of Helicobacter pylori infection.

OBJECTIVE: We prospectively studied an FDA-approved stool test for the diagnosis of Helicobacter pylori infection based on the detection of antigens shed in stool. METHODS: We studied 108 patients undergoing endoscopy. Stool samples were collected on the day of the endoscopy and read in a blinded manner by a technician who was unaware of the findings of the endoscopy. The results of stool testing were compared to those of the rapid urease test (Pyloritek). RESULTS: There were 51 patients infected with H. pylori by rapid urease testing and 57 who were not. The sensitivity of the stool test was 86% (95% confidence interval: 77-96%), the specificity was 91% (81-97%), with a positive predictive value of 89% (77-96%) and a negative predictive value of 88% (81-97%). The likelihood ratio for a positive test was 10.18 and the likelihood ratio for a negative test was 0.11. CONCLUSIONS: The stool test was sensitive and specific for the detection of H. pylori in a U.S. population.

Antigens, Bacterial↗
PubMed2000

Radiologic case study. Rupture of the long head of the biceps tendon.

Rupture of the long head of the biceps tendon frequently is encountered in the setting of coexisting rotator cuff pathology and chronic impingement, but traumatic rupture is occasionally seen, as in this case. Signs and symptoms are not always diagnostic, and MRI or MR arthrography can be a useful tool for evaluation of the tendon in difficult cases. Ideally, an empty bicipital groove is seen, indicating absence of the tendon and rupture. Scar tissue within the groove can be problematic, and correlation with oblique coronal and sagittal images is always recommended. The superior labrum at the attachment of the bicipital anchor should always be inspected carefully, as this is the most common site of rupture, and there may be an associated tear of the superior labrum. Magnetic resonance arthrography is not necessary for diagnosis in most cases, but will provide better visualization of the tendon and bicipital-labral complex.

Accidents, Traffic↗