A structurally conserved water molecule in Rossmann dinucleotide-binding domains

A computational comparison of 102 high-resolution (</=1.90 A) enzyme-dinucleotide (NAD, NADP, FAD) complexes was performed to investigate the role of solvent in dinucleotide recognition by Rossmann fold domains. The typical binding site contains about 9-12 water molecules, and about 30% of the hydrogen bonds between the protein and the dinucleotide are water mediated. Detailed inspection of the structures reveals a structurally conserved water molecule bridging dinucleotides with the well-known glycine-rich phosphate-binding loop. This water molecule displays a conserved hydrogen-bonding pattern. It forms hydrogen bonds to the dinucleotide pyrophosphate, two of the three conserved glycine residues of the phosphate-binding loop, and a residue at the C-terminus of strand four of the Rossmann fold. The conserved water molecule is also present in high-resolution structures of apo enzymes. However, the water molecule is not present in structures displaying significant deviations from the classic Rossmann fold motif, such as having nonstandard topology, containing a very short phosphate-binding loop, or having alpha-helix "A" oriented perpendicular to the beta-sheet. Thus, the conserved water molecule appears to be an inherent structural feature of the classic Rossmann dinucleotide-binding domain.

A conformational analysis of leucine enkephalin as a function of pH

The conformations of Leu enkephalin in aqueous solution have been investigated as a function of pH using molecular dynamics simulations. The simulations suggest the peptide backbone exists as a mixture of folded and unfolded forms (approximately 50% each) at neutral pH, but is always unfolded at low or high pH. The folded form at neutral pH possesses a 2 --> 5 hydrogen bond and a close head to tail separation. No significant intramolecular hydrogen bonding of the carbonyl oxygens was observed in either the folded or unfolded forms of the peptide. Analysis of the Gly carbonyl oxygens and terminal groups indicated that, while the conformational population distribution of Leu enkephalin did vary noticeably as a function of pH, their hydration was essentially independent of pH and in agreement with the available NMR data. Further study indicated that the unfolded state of the peptide was not random in nature and consisted of one major unfolded backbone arrangement stabilized by a persistent hydrophobic interaction between the side chains of Tyr and Leu.

High throughput peptide mass fingerprinting and protein macroarray analysis using chemical printing strategies

We describe a chemical printer that uses piezoelectric pulsing for rapid, accurate, and non-contact microdispensing of fluid for proteomic analysis of immobilized protein macroarrays. We demonstrate protein digestion and peptide mass fingerprinting analysis of human plasma and platelet proteins direct from a membrane surface subsequent to defined microdispensing of trypsin and matrix solutions, hence bypassing multiple liquid-handling steps. Detection of low abundance, alkaline proteins from whole human platelet extracts has been highlighted. Membrane immobilization of protein permits archiving of samples pre-/post-analysis and provides a means for subanalysis using multiple chemistries. This study highlights the ability to increase sequence coverage for protein identification using multiple enzymes and to characterize N-glycosylation modifications using a combination of PNGase F and trypsin. We also demonstrate microdispensing of multiple serum samples in a quantitative microenzyme-linked immunosorbent assay format to rapidly screen protein macroarrays for pathogen-derived antigens. We anticipate the chemical printer will be a major component of proteomic platforms for high throughput protein identification and characterization with widespread applications in biomedical and diagnostic discovery.

Progressive mitochondrial disease resulting from a novel missense mutation in the mitochondrial DNA ND3 gene

We describe a 42-year-old man who presented with a progressive history of epilepsy, stroke-like episodes, bilateral optic atrophy, and cognitive decline. Investigation of his muscle biopsy revealed a specific defect in complex I activity. Subsequent analysis of the mitochondrial genome identified a novel heteroplasmic T10191C mutation in the ND3 gene. The mutation was present at lower levels in blood from the patient and unaffected maternal relatives and is the first pathogenic mitochondrial DNA mutation in the ND3 gene to be described.

Osteoporosis prevention in myasthenia gravis: a reminder

OBJECTIVES

Consensus guidelines for bone management of patients taking corticosteroids suggest two main interventions: Dual energy X-ray absorptiometry (DEXA) scanning in those taking prednisolone > or =7.5 mg daily for > or =6 months (repeated every 1-3 years as indicated). Bisphosphonate therapy for those taking prednisolone > or =15 mg daily for > or =6 months regardless of DEXA result, and also for patients with known or high risk of developing osteoporosis (including those aged >65 years).

MATERIAL AND METHODS

We audited adherence to these guidelines in all adults with myasthenia gravis (MG) attending our neurology service.

RESULTS

Of 80 patients with MG (47 male, mean age 63.3 years), 34 (43%) had received corticosteroids for > or =6 months. Eighteen were taking prednisolone > or =7.5 mg daily (mean dose 16.6 mg) yet only 4 of these (22%) had undergone DEXA scanning. Of the 13 patients meeting the guideline criteria to receive bisphosphonate therapy, this was prescribed to only 7 (54%). Two others were prescribed vitamin D, 2 a calcium supplement and 2 were receiving no prophylaxis.

CONCLUSION

In these MG patients the guidelines were followed in only a minority. Neurologists need greater awareness of the bone health consequences of prescribing long-term corticosteroids.

Clinical recommendations for oxcarbazepine

Oxcarbazepine (OXC) is indicated for treating partial-onset with or without secondary generalized tonic-clonic seizures, in both adults and children aged over 6 years, as monotherapy or adjuvant therapy. Trials data and extensive clinical experience demonstrate generally good tolerability and antiepileptic efficacy similar to carbamazepine (CBZ), sodium valproate or phenytoin. Since the UK launch of OXC in March 2000, UK collaborators have pooled experience to optimize prescribing recommendations for adults. Many patients are successfully managed using the prescribing information recommended titration schedule. However, evolving clinical experience suggests a slower introduction is preferable (e.g. 150 mg day one, then 300 mg daily, increased by 300 mg weekly) both for monotherapy and adjuvant therapy. Overnight 'switch' from CBZ to OXC (using CBZ:OXC ratio of 1:1.5) has been used for patients responsive to CBZ, but with dose-related side-effects. Owing to individual variations in CBZ enzyme autoinduction, however, overnight switching is advised only for those on CBZ < 800 mg daily; otherwise, slower switching is recommended. OXC is not the first choice alternative for patients developing a CBZ rash owing to increased OXC rash rate in CBZ sensitive subjects. Hyponatraemia may be more common (albeit often asymptomatic) than trials data suggest, especially in the elderly. Serum sodium monitoring is unnecessary, however, unless relevant risk factors or pointers exist. Severe haematological dyscrasias have not been reported with OXC. The enzyme inducing interaction of OXC with ethinyloestradiol and levonorgestrel necessitates additional precautions for women using hormonal contraception.

Residence times of water molecules in the hydration sites of myoglobin

Hydration sites are high-density regions in the three-dimensional time-averaged solvent structure in molecular dynamics simulations and diffraction experiments. In a simulation of sperm whale myoglobin, we found 294 such high-density regions. Their positions appear to agree reasonably well with the distributions of waters of hydration found in 38 x-ray and 1 neutron high-resolution structures of this protein. The hydration sites are characterized by an average occupancy and a combination of residence time parameters designed to approximate a distribution of residence times. It appears that although the occupancy and residence times of the majority of sites are rather bulk-like, the residence time distribution is shifted toward the longer components, relative to bulk. The sites with particularly long residence times are located only in the cavities and clefts of the protein. This indicates that other factors, such as hydrogen bonds and hydrophobicity of underlying protein residues, play a lesser role in determining the residence times of the longest-lived sites.