Preferential binding effects on protein structure and dynamics revealed by coarse-grained Monte Carlo simulation

The effect of preferential binding of solute molecules within an aqueous solution on the structure and dynamics of the histone H3.1 protein is examined by a coarse-grained Monte Carlo simulation. The knowledge-based residue-residue and hydropathy-index-based residue-solvent interactions are used as input to analyze a number of local and global physical quantities as a function of the residue-solvent interaction strength (f). Results from simulations that treat the aqueous solution as a homogeneous effective solvent medium are compared to when positional fluctuations of the solute molecules are explicitly considered. While the radius of gyration (R_g) of the protein exhibits a non-monotonic dependence on solvent interaction over a wide range of f within an effective medium, an abrupt collapse in R_g occurs in a narrow range of f when solute molecules rapidly bind to a preferential set of sites on the protein. The structure factor S(q) of the protein with wave vector (q) becomes oscillatory in the collapsed state, which reflects segmental correlations caused by spatial fluctuations in solute-protein binding. Spatial fluctuations in solute binding also modify the effective dimension (D) of the protein in fibrous (D ∼ 1.3), random-coil (D ∼ 1.75), and globular (D ∼ 3) conformational ensembles as the interaction strength increases, which differ from an effective medium with respect to the magnitude of D and the length scale.

A flexible approach for understanding protein stability

A distance constraint model (DCM) is presented that identifies flexible regions within protein structure consistent with specified thermodynamic condition. The DCM is based on a rigorous free energy decomposition scheme representing structure as fluctuating constraint topologies. Entropy non-additivity is problematic for naive decompositions, limiting the success of heat capacity predictions. The DCM resolves non-additivity by summing over independent entropic components determined by an efficient network-rigidity algorithm. A minimal 3-parameter DCM is demonstrated to accurately reproduce experimental heat capacity curves. Free energy landscapes and quantitative stability-flexibility relationships are obtained in terms of global flexibility. Several connections to experiment are made.

Crowns and extra-coronal restorations: considerations when planning treatment

Considerations when planning treatment is the third in the series of crowns and other extra-coronal restorations. Articles or chapters on treatment planning in restorative dentistry can make pretty dry reading, often built around a list of factors that might influence your decision-making. In truth though, planning and placing crowns or other extra-coronal restorations cannot be distilled into a series of lists. The decision-making involved requires experience, subtle understanding and a flexible approach, none of which come easily.

Protein flexibility and dynamics using constraint theory

A new approach is presented for determining the rigid regions in proteins and the flexible joints between them. The short-range forces in proteins are modeled as constraints and we use a recently developed formalism from graph theory to analyze flexibility in the bond network. Forces included in the analysis are the covalent bond-stretching and bond-bending forces, salt bridges, and hydrogen bonds. We use a local function to associate an energy with individual hydrogen bonds, which then can be included or excluded depending on the bond strength. Colored maps of the rigid and flexible regions provide a direct visualization of where the motion of the protein can take place, consistent with these distance constraints. We also define a flexibility index that quantifies the local density of flexible or floppy modes, in terms of the dihedral angles that remain free to rotate in each flexible region. A negative flexibility index provides a measure of the density of redundant bonds in rigid regions. A new application of this approach is to simulate the maximal range of possible motions of the flexible regions by introducing Monte Carlo changes in the free dihedral angles, subject to the distance constraints. This is done using a method that maintains closure of the rings formed by covalent and hydrogen bonds in the flexible parts of the protein, and van der Waals overlaps between atoms are avoided. We use the locus of the possible motions of HIV protease as an example: movies of its motion can be seen at http://www.pa.msu.edu/~lei.

Protein flexibility predictions using graph theory

Techniques from graph theory are applied to analyze the bond networks in proteins and identify the flexible and rigid regions. The bond network consists of distance constraints defined by the covalent and hydrogen bonds and salt bridges in the protein, identified by geometric and energetic criteria. We use an algorithm that counts the degrees of freedom within this constraint network and that identifies all the rigid and flexible substructures in the protein, including overconstrained regions (with more crosslinking bonds than are needed to rigidify the region) and underconstrained or flexible regions, in which dihedral bond rotations can occur. The number of extra constraints or remaining degrees of bond-rotational freedom within a substructure quantifies its relative rigidity/flexibility and provides a flexibility index for each bond in the structure. This novel computational procedure, first used in the analysis of glassy materials, is approximately a million times faster than molecular dynamics simulations and captures the essential conformational flexibility of the protein main and side-chains from analysis of a single, static three-dimensional structure. This approach is demonstrated by comparison with experimental measures of flexibility for three proteins in which hinge and loop motion are essential for biological function: HIV protease, adenylate kinase, and dihydrofolate reductase.

Cyclosporin and the gingival tissues

Cyclosporin is a selective immunosuppressant that has a variety of applications in medical practice. Like phenytoin and the calcium channel blockers, the drug is associated with gingival overgrowth. This review considers the pharmacokinetics, pharmacodynamics, uses and unwanted effects of cyclosporin, in particular the action of the drug on the gingival tissues. Clinical and cell culture studies suggest that the mechanism of gingival overgrowth is a result of an interaction between the drug and its metabolites with susceptible gingival fibroblasts. Plaque-induced gingival inflammation appears to enhance this interaction.

Diagnosis-related groups--application in a paediatric department

The Diagnosis-Related Groups (DRG) system is used in the USA to classify patients on the basis of diagnosis into medically meaningful groups. The system was developed for evaluation of resource utilisation for peer review purposes. It has become better known through being utilised by Medicare, the medical insurance system for the poor in the USA, for prospective determination and payment of patient's hospitalisation costs. A pilot study to compare the costs of hospital care in a sample of the paediatric patient population at Ga-Rankuwa Hospital with the DRG weightings was undertaken to assess its application locally. A poor correlation was found. The costing studies conducted for this purpose were also used to compare resource use between units in the Department of Paediatrics, and substantial unexplained variations were found. It is concluded that the weightings used in the US DRG system cannot be directly applied to the patients at Ga-Rankuwa Hospital for billing purposes. The DRG principle, however, is feasible and has important management benefits; it is recommended that locally determined DRG weightings be developed, and that other hospitals explore their use in peer review of resource management, costing and pricing.

An evaluation of the effectiveness and patient compliance with plaque control methods in the prevention of periodontal disease

The study was designed to evaluate the effectiveness of plaque control recommendations 6 months following active treatment of moderately advanced periodontal disease in 100 patients. The compliance of the patients to the use of different numbers of plaque control aids was also assessed. Our observations suggest that oral hygiene standards deteriorate during periods of unsupervised maintenance, and this is unrelated to either the number of aids recommended or the number of treatment visits. The reasons for patients failing to comply with professional recommendations were determined.

Effect of single dose aspirin on the development of penile hypercoagulability during erection

The effect of aspirin on the development of hypercoagulability in the penile blood during erection was studied in five Chacma baboons. Aspirin prevented the generation of hypercoagulability and may be of importance in delaying the development of penile atherosclerosis and ageing impotence.

Entrapment of platelets in the penis during and after erection

Because of the development of hypercoagulability and the deposition of fibrin in the penis during erection a study of the possible role of platelets in this process was undertaken. Platelet response was studied in 9 adult chacma baboons (Papio ursinus) using autologous in vitro indium-111-labelled platelets and sequential scintigraphy of the penis during erection. The blood pooling pattern was obtained using in vivo technetium-99m-labelled red cells in a similar investigation. A statistically significant retention of platelets occurred during and after erection, which could not be attributed to blood pooling (P less than 0,05). Entrapment of platelets could lead to enhanced activity and activation, and might play a significant role in hypercoagulability and fibrin deposition during erection. Therefore platelets could be an important factor in the pathogenesis of ageing impotence.

Thromboxane B2 production during erection

The effect of erection on 6-keto-PGF1 alpha and thromboxane B2 in penile blood during electrically evoked erection was studied in the chacma baboon. 6-keto-PGF1 alpha remained at a low concentration, but thromboxane B2 showed a statistically significant rise 8-10 minutes after commencement of erection. Elevated thromboxane B2 during erection may potentiate platelet aggregation and may be one of the key events in the pathogenesis of ageing impotence.

The sebaceous gland antigen defined by the OM-1 monoclonal antibody is expressed at high density on the surface of ovarian carcinoma cells

A monoclonal antibody, designated OM-1, was raised against ovarian serous papillary cystadenocarcinoma (stage IV) cells. This antibody was found to react strongly with primary and metastatic ovarian serous cystadenocarcinomas and endometrioid carcinomas but the antigen detected was either absent or at very low levels in ovarian mucinous adenocarcinomas, clear cell carcinomas, benign serous and mucinous cystadenomas and Brenner tumours. The OM-1 antibody gave no detectable reaction with 93 other human tumours, including examples of breast and colon adenocarcinomas. In normal tissues the OM-1 antibody reacted with normal sebaceous gland cells, lung type II pneumocytes and placental syncytial trophoblasts. In the normal ovary OM-1 reactivity was confined to extremely weak staining of the surface epithelium. No reaction with any other ovarian cell type could be detected. No evidence of reaction with other normal cell populations present in 24 adult and seven foetal tissues was found. The antigen detected is compared with other ovarian tumour-associated antigens. The OM-1 antibody is likely to prove of value in the detection and diagnosis of ovarian carcinoma.

Evaluation of the diagnostic efficacy of autologous 111In-labelled platelets as a scanning agent for deep vein thrombosis in the chacma baboon

The diagnostic efficiency of autologous 111In-labelled platelets (ILP) as a scanning agent in deep vein thrombosis (DVT) was investigated in 24 South African baboons (Papio ursinus). Thrombi were surgically induced by stasis, intimal injury and the injection of thrombin in the common femoral veins of adult baboons. The thrombi were allowed to age for 1, 2, 4, 8, 24, 48 and 72 h before injecting the ILP. Scanning was done with a large field gamma camera at 10 min post injection and again at 2, 4, 6, 8, 10, 14, 24, 48 and 72 h. Time-activity curves were thus obtained and it was possible to establish an optimal time after injection of the ILP to scan for each group of thrombi. The results indicate that only the younger thrombi (1-8 h after thrombus formation) were detected. Twenty-four hour and older thrombi were not visualised. A favourable time to scan in the case of the younger thrombi appeared to be approximately 20 h after the injection of ILP. However, the thrombus age limitation still impairs the diagnostic efficiency of the procedure.

Monoclonal anti-T-cell antibodies react with circulating myeloid leukemia cells and normal tissue macrophages

Rabbit and monoclonal antibodies to human myeloid leukemia cells, monocytic leukemia cells and human thymocytes have shown the existence of common T-cell/myeloid/monocyte antigens. For this reason, the specificity of a series of monoclonal antibodies to human T-cells (OKT 1, 3, 4, 5, 6, 8, 9, 10; and NA1/34) was tested by immunofluorescence (cytofluorograph) and complement-mediated cytotoxicity against human myeloid leukemia and normal blood cells and leukemic cell lines. In addition, an immunohistological analysis of the specificity of OKT4, 9.3, Leu 3a, OKT3 and NA1/34 antibodies was performed using normal lymphoid tissues and a sensitive immunoperoxidase technique. Normal human peripheral blood mononuclear cells reacted with OKT3 ("pan T-cell", mean 54%), OKT4 ("helper T-cell", mean 35%) and OKT 5/8 ("suppressor T-cell", mean 18%) as previously reported. However, OKT3 reacted with the cell lines K562 (myeloid), RC2a and THP-1 (monocytoid) and U937 (macrophage) as well as with cells from 9/65 myeloid leukemia patients. OKT4 reacted with the cell lines HL60 (promyelocyte), RC2a and U937 and also with cells from 6/60 myeloid leukemia patients. OKT5 reacted with the cell lines K562 and THP-1. OKT1 ("pan T-cell") reacted with THP-1 and with myeloid and monocytic leukemia samples (5/32) as did OKT6 ("cortical thymocyte") (3/32). OKT10 ("common thymocyte") reacted with a range of leukemia cell lines (B-cell, pre- B-cell and macrophage) as well as 7/21 myeloid leukemia samples. In tissue sections Leu 3a, (9.3 and OKT4 to a lesser extent), stained paracortical lymphocytes, plus subcapsular and medullary macrophages, and dendritic cells present within the paracortex.(ABSTRACT TRUNCATED AT 250 WORDS)

A clinical investigation into the incidence of dry socket

A clinical investigation was undertaken to find the incidence of dry socket as a post-operative complication of dental extraction on an out-patient basis. Two thousand three hundred and sixty three extractions were carried out under local anaesthesia by clinical staff and students over a four month period. The results are presented and their significance discussed, the incidence of dry socket being found to be dependent upon the site of the tooth extracted, the relative difficulty of the extraction and upon the integrity and size of the blood clot in the extraction socket.

Standardisation of tracer and type of meal in the evaluation of gastric emptying and colon transit rates in normal beagle dogs

The transit 111In-labelled polymer beads of different particle sizes in the stomach and colon of five healthy Beagle dogs was monitored after intake of different kinds of meal by a gamma camera and data processor system. The various meals studied were a solid balanced type of dog food mixed with milk, pure milk, and finally a meal of raw meat. The polymer beads carried triethylenetetramine type functions which efficiently chelated 111In+3 from an aqueous solution of InCl3. These labelled beads were well mixed into the food before being offered to the dogs. Gastric emptying curves from which half-times of emptying (T 1/2) could be obtained are presented and statistically compared. Good quality images with quantification of the colon transit rate also became possible. It appeared that standardisation of the tracer and of the meal is compulsory for relevant and reproducible results.