Characterization of the ternary complex between Rab7, REP-1 and Rab geranylgeranyl transferase

Geranylgeranylation is a post-translational modification of Rab GTPases that enables them to associate reversibly with intracellular membranes. Geranylgeranylation of Rab proteins is critical for their activity in controlling intracellular membrane transport. According to the currently accepted model for their action, newly synthesized Rab proteins are recruited by Rab escort protein (REP) and are presented to the Rab geranylgeranyl transferase (RabGGTase) which covalentely modifies the Rab protein with two geranylgeranyl moieties. After prenylation, the Rab protein remains in complex with REP and is delivered to the target membrane by the latter. In this work, we show that RabGGTase can form a stable complex with Rab7-REP in the absence of its lipid substrate geranylgeranyl pyrophosphate. In order to characterize this interaction, we developed three fluorescence assays reporting on the interaction of RabGGTase with the Rab7-REP complex. For this interaction we determined a Kd value of about 120 nM. Association of RabGGTase with the Rab7-REP complex occurs with a rate constant of approximately 108 M-1 x s-1. We demonstrate that the state of the nucleotide bound to Rab7 does not influence the affinity of RabGGTase for the Rab7-REP-1 complex. Finally, we address the issue of substrate specificity of RabGGTase. Titration experiments demonstrate that, in contrast with farnesyl transferase, RabGGTase does not recognize a defined C-terminal sequence motif. Experiments using Rab7 mutants in which the last 16 amino acids were either mutated or truncated revealed that the distal part of the C-terminus makes only a limited contribution to the binding affinity between RabGGTase and the Rab7-REP-1 complex. This demonstrates the functional dissimilarity between RabGGTase and geranylgeranyl transferase I and farnesyl transferase, which interact specifically with the C-terminus of their substrates. Based on these experiments, we propose that RabGGTase recognizes the overall structure arising from the association of Rab and REP and then 'scans' the flexible C-terminus to position the proximal cysteines into the active site.

Prostatic growth rate determined from MRI data: age-related longitudinal changes

Men with prostatic enlargement are at highest risk of developing symptomatic lower urinary tract symptoms (LUTS) and related outcomes, such as acute urinary retention. The study of prostatic growth rate can identify the age range at which prostate growth peaks. Evaluation of the natural course of prostate growth requires repeated intraindividual volume measurements at time intervals sufficient to document growth. Our objective was to examine age-stratified prostate growth rates from men taking part in a longitudinal study of aging using magnetic resonance imaging (MRI) of the prostate. Sixty-four men (ages 30-71 years) enrolled in the Baltimore Longitudinal Study of Aging (BLSA) who had T2 pelvic MRIs taken approximately every 2 years were studied. Men were age stratified into four groups: <45, 45-55, 56-65, and >65 years old. Whole prostate and central gland (anatomically referred to as the transition zone) volumes were determined from the MRI images by a semi-automated image analysis program. Peripheral gland volumes were calculated as the difference between whole prostate and central gland volumes. Growth rates (cc per year) were calculated as change in volume divided by the time interval. On the basis of measurements from the T2 images (n = 128), we observed a linear trend between prostate volume and age. The overall prostate growth rate was 2.36 +/- 3.52 cc per year. Age-stratified growth rates revealed that prostate growth increased with age, peaked at 4.15 +/- 4.98 cc/year for the 56-65-year-old age group and then declined rapidly for the older-aged men. The central gland growth rates followed a trend similar to total prostate volume. These data suggest that there is an age-related increase in prostate growth rate that peaks in men ages 56-65 and then declines. Identification of this trend in prostate growth may aid physicians in targeting men for early diagnosis of LUTS and for possible early intervention. Future studies with a larger sample size are necessary to substantiate these findings.

[How are palliative care needs estimated in short-stay establishments? Apropos of an experience in Côte d'Or]

The evaluation of needs and means concerning the care of patients in palliative treatment is among the problems seen as priority by the High Committee for Public Health. We have thus tried to characterise, in a specific health sector, the patients receiving palliative care in short-stay establishments in order to evaluate their care needs. We carried out an exhaustive descriptive survey among all public and private short-stay establishments in the Côte d'Or region. Of the 2116 patients in the hospital on the day of the survey, roughly 30% were considered as eligible for palliative care (patients suffering from serious, chronic and progressive illnesses). The average age of these patients is 63.9 years (standard deviation 19.7). They mainly suffer from tumours (50%), circulatory pathologies (15%), mental illness (7%), or neurological illnesses (6%). Among the patients that may need palliative care, 38% say they feel pain despite treatment with pain-killers among 25.3% of them. The personnel providing care is insufficiently trained in palliative care or in pain, as only a maximum of 18% of nurses and 5% of doctors in short-stay establishments have been trained in these areas.

Sylvian aqueduct syndrome and global rostral midbrain dysfunction associated with shunt malfunction

OBJECT

This study is a retrospective analysis of clinical data obtained in 28 patients affected by obstructive hydrocephalus who presented with signs of midbrain dysfunction during episodes of shunt malfunction.

METHODS

All patients presented with an upward gaze palsy, sometimes associated with other signs of oculomotor dysfunction. In seven cases the ocular signs remained isolated and resolved rapidly after shunt revision. In 21 cases the ocular signs were variably associated with other clinical manifestations such as pyramidal and extrapyramidal deficits, memory disturbances, mutism, or alterations in consciousness. Resolution of these symptoms after shunt revision was usually slow. In four cases a transient paradoxical aggravation was observed at the time of shunt revision. In 11 cases ventriculocistemostomy allowed resolution of the symptoms and withdrawal of the shunt. Simultaneous supratentorial and infratentorial intracranial pressure recordings performed in seven of the patients showed a pressure gradient between the supratentorial and infratentorial compartments, with a higher supratentorial pressure before shunt revision. Inversion of this pressure gradient was observed after shunt revision and resolution of the gradient was observed in one case after third ventriculostomy. In six recent cases, a focal midbrain hyperintensity was evidenced on T2-weighted magnetic resonance imaging sequences at the time of shunt malfunction. This rapidly resolved after the patient underwent third ventriculostomy.

CONCLUSIONS

It is probable that in obstructive hydrocephalus, at the time of shunt malfunction, the development of a transtentorial pressure gradient could initially induce a functional impairment of the upper midbrain, inducing upward gaze palsy. The persistence of the gradient could lead to a global dysfunction of the upper midbrain. Third ventriculostomy contributes to equalization of cerebrospinal fluid pressure across the tentorium by restoring free communication between the infratentorial and supratentorial compartments, resulting in resolution of the patient's clinical symptoms.

[Psychiatric hospitalizations after the June 27 1990 Law in a French department]

The law, edicted on the 27th june 1990, has introduced in France the without consent hospitalization, to replace the law of 30th june 1838 which was composed of confinements or psychiatric placings. On of the both new types of a without consent admission, called "by a third person request" hospitalization (HDT) containing a procedure called "usual" and another one called "situation emergency", appeared to us more and more used in our practice, particularly the "situation emergency" HDT. Therefore we compared on three periods, one before the law, the two others ones 3 and 6 years after it, the different types of psychiatric admissions in all of the seven psychiatric sectors of a french department. All the hospitalization's forms increase with the chronologic time in Côte d'Or. We notice too in this department an important increase of the HDT, but especially in the "situation emergency" ones, and this, with a statistically revealing way compared to the other types of admission. If this phenomena wasn't purely localized, which only the departmental commissions of psychiatric hospitalization, created by the 1990's law, can reveal by proceeding to an expected assessment of the law consequences, the legislator should fastly take this evolution into account.

Principles governing amino acid composition of integral membrane proteins: application to topology prediction

A new method is suggested here for topology prediction of helical transmembrane proteins. The method is based on the hypothesis that the localizations of the transmembrane segments and the topology are determined by the difference in the amino acid distributions in various structural parts of these proteins rather than by specific amino acid compositions of these parts. A hidden Markov model with special architecture was developed to search transmembrane topology corresponding to the maximum likelihood among all the possible topologies of a given protein. The prediction accuracy was tested on 158 proteins and was found to be higher than that found using prediction methods already available. The method successfully predicted all the transmembrane segments in 143 proteins out of the 158, and for 135 of these proteins both the membrane spanning regions and the topologies were predicted correctly. The observed level of accuracy is a strong argument in favor of our hypothesis.

Socio-economic impact of chronic venous insufficiency. An underestimated public health problem

BACKGROUND

Disease of the venous system is an underestimated public health problem affecting all Western industrialised countries. The prevalence of venous disease of the lower limb in the adult population is estimated at 40-50% for men and 50-55% for women, whereas visible varicose veins and chronic venous insufficiency are, respectively, present in 10-15% and 2-7% of the male population and 20-25% and 3-7% of the female population. In France the costs of venous disease represented 2.6% of the total health care budget in 1995, thus confirming other data from European studies and an early health survey in the USA. To evaluate the socio-economic impact of chronic venous insufficiency by measuring the health care cost.

METHODS

Detailed information on diagnostic and therapeutic procedures for venous disease was obtained from the billing data of the compulsory health insurance system in Belgium. Total ambulatory and intramural treatment costs are calculated for varicose veins of the lower limb and for haemorrhoids during the 1988-1995 period.

RESULTS

Medical care costs for chronic venous disease amount to 10 billion BEF, which is 2-2.5% of the 1995 total health care budget. Annual spending on venotropic drugs with 11.5 mean daily doses per 1,000 inhabitants amounted to one billion BEF in 1995 for ambulatory treatment only.

CONCLUSIONS

In view of the major medical, social and economical consequences of venous pathology, research and prevention efforts are required in this area as part of a well-targeted and effective health policy.

Rod models of DNA: sequence-dependent anisotropic elastic modelling of local bending phenomena

Local bending phenomena can be predicted by elastic models that incorporate sequence-dependent anisotropic-bendability (SDAB). SDAB models consider DNA to be an initially straight, segmented, elastic rod, in which the flexibility of each segment is greater towards the major groove than it is in other directions. While local bending can be predicted by static-geometry models as well, SDAB models, in addition, qualitatively explain such phenomena as the affinity of protein binding and kinking. A set of prediction tools is available at http:/(/)www.icgeb.trieste.it/dna.

GLUT1 gene polymorphism in non-insulin-dependent diabetes mellitus: genetic susceptibility relationship with cardiovascular risk factors and microangiopathic complications in a Mediterranean population

OBJECTIVE

It has been suggested that the polymorphic variation of GLUT1 glucose transporter may contribute to genetic susceptibility to type 2 diabetes in some populations. We have evaluated the GLUT1-XbaI polymorphism in an association study of a Caucasian Mediterranean population and its role in the susceptibility to displaying either microangiopathic complications or any of the risk factors associated with type 2 diabetes.

RESEARCH DESIGN AND METHODS

A total of 193 type 2 diabetic patients (104 women and 89 men, 31-82 years of age, diabetes duration 13.2 +/- 6.2 years) and 90 healthy subjects (48 women and 42 men, 20-72 years of age) were recruited for the association study. For the evaluation of nephropathy and retinopathy, type 2 diabetic patients were matched with those not having microangiopathic complications.

RESULTS

Genotypic or allelic frequencies did not differ significantly between controls and type 2 diabetic patients. Regarding the distribution of clinical or metabolic parameters according to GLUT1 genotype, patients with X1X1 genotype tended to have higher diastolic blood pressure levels compared with the remaining genotypes (P = 0.008). There were no differences in genotypic or allelic distribution among patients for either the presence or absence of retinopathy or nephropathy.

CONCLUSIONS

We conclude that GLUT1 loci did not contribute significantly to type 2 diabetes in this cohort and is not a determinant for cardiovascular risk factors or chronic microangiopathic complications associated with type 2 diabetes. The weak association with diastolic hypertension must be confirmed in other populations.

Preschool stunting, age at menarche and adolescent height: a longitudinal study in rural Senegal

OBJECTIVE

To study the impact of preschool stunting on adolescent height and age at menarche in rural West Africa.

DESIGN

A longitudinal, population-based study.

SETTING

The Niakhar study area in Central Senegal.

SUBJECTS

1650 children aged 12-17 y with known height-for-age at the age of 2-5 y.

MAIN OUTCOME MEASURES

Adolescent height; mean age at menarche of girls estimated by the status quo method.

RESULTS

The subjects were divided into three groups of preschool height-for-age: < -2, -2 to -1 and > -1 z-score of the NCHS reference. The mean height during adolescence differed significantly according to preschool height-for-age for both boys and girls (P < 0.001). Relative risk of adolescent stunting according to preschool stunting varied from 2.0-4.0 depending on age and sex. Estimated mean age at menarche was 17.2 (95% fiducial confidence interval: 16.6-18.7), 16.5 (16.1-17.2) and 15.6 (15.2-16.0) y, respectively, for the three groups of preschool height-for-age (P < 0.001). Mean increment from age 5 y to adolescence did not differ significantly among the boys according to preschool stunting, but among the girls aged 16-17 y, the increment was higher for those who had been stunted during preschool life (P < 0.01).

CONCLUSION

Some evidence of catch-up growth between the ages of 5 and 17 y was found for stunted girls. The significant delay in sexual maturation of the stunted girls suggests that stunted children of both sexes have a possibility of catch-up growth after the age of 17 y.

[Pharmaco-economics: a point of view of the mutualities]

In Belgium, the mutualities are responsible for their budgets. They are playing an important role in drug pricing and reimbursement procedures. This document aims at explaining our line of arguments for a critical evaluation and the place for a pharmacoeconomic evaluation in the Belgian social security system. The available economic data for each molecule or pathology are essential but insufficient. Economic evaluations could help to reveal the costs and benefits of different uses of medical therapies and could thereby enhance the resources allocation in a health care system. But this science is still in its infancy, and in practice, the methodological quality of this kind of study is often weak. Furthermore it is not easy to transfer those evaluations to the Belgian reimburse systems. The clinical efficacy and the transparency is price setting should remain the two most important criterions to build reimbursement rules in order to ensure right price, rational use of medicine and accessibility for all.

Moderate discrimination of REP-1 between Rab7 x GDP and Rab7 x GTP arises from a difference of an order of magnitude in dissociation rates

The kinetics of the interaction of Rab7 with REP-1 have been investigated using the fluorescence of GDP and GTP analogs at the active site of Rab7. The results show that REP-1 has higher affinity for the GDP bound form of Rab7 (Kd=1 nM) than for the GTP bound form (Kd=20 nM). Both affinities should still be sufficient for the formation of stable complexes in the cell. The association reaction proceeds in two steps for the GDP bound form. The initial step is fast (k+1 = ca. 10[7] M[-1] s[-1]) and concentration dependent while the second represents a slow equilibration (k+2 + k-2 = 3.5 s[-1]) which has little effect on the overall equilibrium. The difference in affinity of the two nucleotide bound forms arises from a difference in dissociation rates (0.012 s[-1] for Rab7 x GDP and 0.2 s[-1] for Rab7 x GTP).

Automated image analysis system for detecting boundaries of live prostate cancer cells

Image analysis provides a powerful tool for quantifying cell motility and has been used to correlate motility with metastatic potential in an animal model of prostate cancer. However, widespread use of this image analysis method has been limited because earlier methods of quantitative analysis required time-intensive and subjective manual tracing of cell contours. In this report, we describe a fully automated image segmentation algorithm for detection and morphometric description of prostatic cells. The segmentation system was tested on prostate cell images generated from Hoffman modulation contrast microscopy (47 cells at 64 time points = 3,008 images) and differential interference contrast microscopy (29 cells at 64 times points plus 1 cell at 62 time points = 1,918 images). Morphometric measurements were derived from computer-determined cell boundaries and compared with the same measurements derived from manually traced cell boundaries. Final correlation coefficients for area and perimeter measurements for Hoffman and differential interference contrast microscopy were (0.76, 0.62) and (0.93, 0.93), respectively. Results with our differential interference contrast images demonstrate that our segmentation algorithm reliably and efficiently replaces the need for manually traced cell boundaries in addition to eliminating intraobserver variation. Our automated segmentation process will have immediate utility in our motility analysis system that relates cell motility with metastatic potential of prostate cancer.

The role of DNA bending in Cro protein-DNA interactions

Binding energy of DNA-Cro protein complexes is analyzed in terms of DNA elasticity, using a sequence-dependent anisotropic bendability (SDAB) model of DNA, developed recently [M.M. Gromiha, M.G. Munteanu, A. Gabrielian and S. Pongor, J. Biol. Phys. 22(1996) 227-243.]. The protein is considered to bind aspecifically to DNA that reduces the freedom of movement in the DNA molecule. In cognate DNA, the Cro protein moves on to form specific interactions and bends DNA. A comparison of the experimental data [Y. Takeda, A. Sarai and V.M. Rivera, Proc. Natl. Acad. Sci. U.S.A. 86 (1989) 439-443.] with the calculated DNA stiffness data shows that delta G of the complex formation increases with stiffness of the ligand when the interactions are nonspecific ones, while an opposite trend is observed for specific binding. Both of these trends are in agreement with our approach using the SDAB model. A decomposition of the energy terms suggests that binding energy in the nonspecific case is used maily to compensate the free energy changes due to entropy lost by DNA, while the energy of specific interactions provide enough energy both to bend the DNA molecule and to change the conformation of the Cro protein upon ligand binding.

Nutritional status and age at menarche of Senegalese adolescents

Growth and maturation during adolescence has not been well described in rural African populations, although it may represent the missing link between high levels of preschool stunting and nearly 'normal' adult heights. In 1995 the homes of subjects aged 10.3-17.5 years, living in a rural area of Senegal, were visited, and all adolescents present, 1527 boys and 1126 girls, were included in the analysis. A number of girls were absent because they worked in the capital city Dakar. Resident girls (n = 705) had significantly higher means than boys for all anthropometric variables (weight, body mass index, arm circumference and muscle arm circumference, triceps and subscapular skinfolds), except for height and head circumference. Girls who had just returned from seasonal migration to Dakar (n = 415) were, on average, 2 kg heavier, but not taller, than resident girls (p < 0.0001). The girls fell off in height from 11 to 13 years compared to the NCHS reference and then 'caught up' until the age of 17, while boys fell off during the entire age span. Mean age at menarche was estimated at 16.1 years (95% fiducial CI: 15.8-16.4) from status quo data by probit analysis. No significant difference was found between residents and migrants. Postmenarcheal girls had better nutritional status than premenarcheal girls in terms of height, weight, body mass index, percentage body fat and arm muscle circumference (p < 0.0001). In conclusion, puberty, as assessed by age at menarche, is delayed by about 3 years in this population, probably due to malnutrition.

Stabilization centers in proteins: identification, characterization and predictions

Methods are presented to locate residues, stabilization center elements, which are expected to stabilize protein structures by preventing their decay with their cooperative long range interactions. Artificial neural network-based algorithms were developed to predict these residues from the primary structure of single proteins and from the amino acid sequences of homologous proteins. The prediction accuracy using only single sequence information is 65%, but the incorporation of evolutionary information in the form of multiple alignments and conservation scores raises the efficiency by 3%. The composition, relative accessibility, number and type of interactions, conservation and the X-ray thermal factor of the identified stabilization center residues are different, not only from the whole data set but from the rest of the long range interacting residues as well. The most frequent stabilization center residues are usually found at buried positions and have a hydrophobic or aromatic side-chain, but some polar or charged residues also play an important role in the stabilization. The stabilization centers show significant difference in the composition and in the type of linked secondary structural elements compared with the rest of the residues. The performed structural and sequential conservation analysis showed the higher conservation of stabilization centers over protein families. The relation of the proposed stabilization centers to folding nuclei is also discussed.

[Cholelithiasis following gastric surgery]

A retrospective study was carried out in order to verify the correlation between the biliary disease and previous gastroduodenal operations for various lesions. The 24 patients (18 males and 6 females with an average age of 54 years) reported were diagnosed with chronic or acute cholelithiasis (with common bile duct stones and cholangitis) which imposed emergency or short delayed surgery in most of the cases. The previous gastric operations performed 5 up to 23 years ago were classic gastrectomies with Polya (9 cases) or Péan (8 cases) anastomosis, truncal vagotomy with pyloroplasty or gastroenterostomy for gastric and duodenal ulcers, one hemigastrectomy, one antrectomy and one tumorectomy for benign gastric tumours (one schwannoma and two polyps), one enlarged subtotal gastrectomy for adenocarcinoma and, finally, one gastrotomy for a suspected bleeding gastric tumour. The causal connection between cholelithiasis and previous gastric surgery is obvious, anatomical changes and alterations in the kinetics of the duodenum and common duct being incriminated.

[Value of helical CT scan in the preoperative assessment of the ureteropelvic junction syndrome]

INTRODUCTION

The search for anatomical variants of the renal blood supply is an important element in the choice of surgical technique for the treatment of ureteropelvic junction syndrome.

MATERIAL AND METHODS

Prospective study of 17 patients (mean age: 33 years), assessed by spiral CT with acquisition of overlapping thin sections during the arterial phase. The renal blood supply anatomical findings were then compared with operative findings in all patients.

RESULTS

We observed a solitary renal artery in 8 cases, a lower pole pedicle crossing the junction in 9 cases and vascular abnormalities in 4 cases. All of these radiological findings were confirmed intraoperatively. Spiral CT, with rapid acquisition during the arterial phase and overlapping thin sections, allows accurate analysis of the renal blood supply. Axial sections are sufficient to provide the necessary anatomical information. Three dimensional reconstructions allow a better spatial visualization of the various structures.

CONCLUSION

This examination allows visualization of a possible lower pole artery associated with UPJ syndrome, with identical accuracy to that of renal arteriography, but constitutes a less invasive and less expensive investigation.

The role of long-range interactions in defining the secondary structure of proteins is overestimated

MOTIVATION

Secondary structure predictions based on the properties of individual residues, and sometimes on local interactions, usually fail to exceed 65% efficiency. Therefore, non-local, long-range interactions seem to be a significant cause of this limitation.

RESULTS

In this paper, we apply approaches to localize highly interacting residues and clusters of residues involved in multiple non-local interactions, and test various secondary structure predictions on this separate subset to assess the effect of long-range interactions on the prediction efficiencies. It was found that only a marginal part of the failure of secondary structure predictions results from the presence of long-range interactions. Alternative possibilities are also discussed.

Segmentation algorithms for detecting microcalcifications in mammograms

The presence of microcalcification clusters in mammograms contributes evidence for the diagnosis of early stages of breast cancer. In many cases, microcalcifications are subtle and their detection can benefit from an automated system serving as a diagnostic aid. The potential contribution of such a system may become more significant as the number of mammograms screened increases to levels that challenge the capacity of radiology clinics. Many techniques for detecting microcalcifications start with a segmentation algorithm that indicates all candidate structures for the subsequent phases. Most algorithms used to segment microcalcifications have aspects that might raise operational difficulties, such as thresholds or windows that must be selected, or parametric models of the data. We present a new segmentation algorithm and compare it to two other algorithms: the multi-tolerance region growing algorithm that operates without the aspects mentioned above, and the active contour model that has not been applied previously to segment microcalcifications. The new algorithm operates without threshold or window selection, or parametric data models, and it is more than an order of magnitude faster than the other two.

Prediction of transmembrane alpha-helices in prokaryotic membrane proteins: the dense alignment surface method

A new, simple method for predicting transmembrane segments in integral membrane proteins has been developed. It is based on low-stringency dot-plots of the query sequence against a collection of non-homologous membrane proteins using a previously derived scoring matrix [Cserzö et al., 1994, J. Mol. Biol., 243, 388-396]. This so-called dense alignment surface (DAS) method is shown to perform on par with earlier methods that require extra information in the form of multiple sequence alignments or the distribution of positively charged residues outside the transmembrane segments, and thus improves prediction abilities when only single-sequence information is available or for classes of membrane proteins that do not follow the 'positive inside' rule.

Interresidue interactions in protein classes

The free energy difference between folded and unfolded state is about the same for most proteins and it is not more than the energy of a few noncovalent interactions. In addition to the numerous noncovalent interactions, some proteins contain one or more disulfide bonds, which, as covalent crosslinks, significantly stabilize their tertiary structure. Correlation between the presence of disulfide bond(s), and the number noncovalent interresidue interactions of various kinds is analyzed here. The number of interactions per residue is almost the same for all protein. Also the number of long-range interactions per residue is the same in all proteins. Proteins with S--S bond(s) (extracellular proteins) have more medium-range and fewer short-range interactions than those without S--S bonds. However, the difference is independent of the number of these covalent crosslinks. We concluded that the different distributions of the various kinds of noncovalent interaction reflect the needs of proteins in the different environments, the extracellular and the intracellular ones, rather than the presence of the disulfide bond(s). We also pointed out that the observed differences in the distributions of short- and medium-range interactions are in good agreement with different secondary structure compositions of extracellular and intracellular proteins.

Conservation of amino acids in multiple alignments: aspartic acid has unexpected conservation

Analysis of the relationship between surface accessibility and amino acid conservation in multiple sequence alignments of homologous proteins confirms expected trends for hydrophobic amino acids, but reveals an unexpected difference between the conservation of Asp, Glu and Gln. Even when not in an active site, Asp is more highly conserved than Glu. There is a clear preference for conserved and buried Asp to be present in coil, but there is no tendency for Asp to conserve phi/psi in the ++ region of the Ramachandran map. Glu does not show any preference to be conserved in a particular secondary structure. Analysis of recently derived substitution matrices (e.g. BLOSUM) confirms that Glu tends to substitute more frequently with other amino acids than does Asp. Analysis of relative accessibility versus relative conservation for individual amino acid positions in alignments shows a negative correlation for all amino acid types. With the exception of Arg, Lys, Gly, Glu, Asp and Tyr, a relative conservation of > 2 suggests the amino acid will have a relative accessibility of < 50%. Observation of conserved Cys, Gly or Asp in a reliable multiple alignment suggests a position important for the structure of the protein. Furthermore, the Asp is likely to be involved in polar interactions through its side chain oxygen atoms. In contrast, Gln is the least conserved amino acid overall.

GTPase activity of Rab5 acts as a timer for endocytic membrane fusion

The GTPase cycle is a versatile regulatory mechanism directing many cell functions, and Rab family members use it to regulate intracellular transport. Current models propose that GTP hydrolysis by Rab proteins is either required for membrane fusion or occurs afterwards to allow recycling of the protein. To measure the GTPase activity of Rab5 in endocytic membrane fusion, we engineered a mutant that preferentially binds xanthosine 5'-triphosphate (XTP),Rab5(D136N) and monitored the kinetics of [alpha(32)P]-XTP hydrolysis in situ during endosome fusion in vitro. Surprisingly, nucleotide hydrolysis occurred even in the absence of membrane fusion, indicating that membrane-bound Rab5 undergoes futile cycles of GTP(XTP) binding and hydrolysis. Nucleotide triphosphate hydrolysis by Rab5 is not conditional on membrane fusion and is reduced by its effector Rabaptin-5. Our data reveal that the GTP cycle of Rab proteins differs from that of other GTPases (for example, EF-Tu) and indicate that GTP hydrolysis acts as a timer that determines the frequency of membrane docking/fusion events.

[Pancreatic and extrapancreatic fluid collections following acute and chronic pancreatitis]

Intra- or extrapancreatic liquid collections are common complications for acute and chronic pancreatitis, with variable morphologic features and possible evolution toward complications. A total of 31 liquid collections (pseudocysts, ascites and/ or enzymatic pleurisy) in 22 patients are presented. The study assems the etiology, the diagnostic methods and the treatment of the liquid collections. The preferred surgical treatment is either cysto-digestive anastomosis or distal pancreatic resections. Also some new therapeutic modalities are analyzed percutaneous or endoscopic drainage.

Kinetics of interaction of Rab5 and Rab7 with nucleotides and magnesium ions

We describe here the kinetics of the interaction of GTP and GDP with the small GTP-binding proteins Rab5 and Rab7. It was possible to make use of the intrinsic fluorescence of these proteins, since Rab5 contains two and Rab7 three tryptophan residues, respectively. With both enzymes, there is a significant decrease in fluorescence on binding GTP and an increase on binding GDP. As with the small GTP-binding protein Ha-Ras p21 and with EF-Tu, nucleotide binding occurs in at least two steps and is describable in terms of a relatively weak initial interaction followed by a highly irreversible isomerization of the protein-nucleotide complex, which results in a change in the fluorescence properties. Dissociation of GDP and GTP could be followed in a time-dependent manner using fluorescently labeled GDP (methylanthraniloyl GDP) as displacing agent and taking advantage of substantial fluorescent energy transfer from tryptophan to the nucleotide. Fluorescence techniques could also be used to quantitate the interaction of Mg2+ ions with the GTP and GDP forms of Rab7, and it was shown that the metal ion was bound approximately 1000-fold more strongly to the GTP than the GDP form. The rate of GTP cleavage by the two proteins differed by a factor of approximately 20 (2 x 10(-3)s-1 for Rab5 and 9 x 10(-4)s-1 for Rab7 at 37 degrees C). Both proteins showed significant discrimination against xanthosine 5'-O-diphosphate (Kd approximately 10(3)-fold higher than that of GDP) and dramatic discrimination against ADP or ATP (Kd approximately 10(6)-fold higher than that of GDP). The results demonstrate a high degree of mechanistic similarity between the Rab proteins and other GTP-binding proteins, which have been examined in detail, including Ha-Ras p21, Ran, and EF-Tu.

[Diagnostic value of various echo- and Doppler echocardiography methods in quantifying mitral valve stenosis]

Two-dimensional and Doppler echocardiography have been widely used for noninvasive determination of valve area in patients with mitral stenosis. Recent studies have indicated that the Doppler-echocardiographic pressure half-time method (PHT) does not accurately predict mitral orifice area (MOA). Therefore, applications of the continuity equation and the Gorlin formula have been used additionally to the PHT for Doppler-echocardiographic assessment of MOA. In a prospective study of 34 patients MOA determined by two-dimensional and Doppler echocardiography was compared with MOA measured by cardiac catheterization (range 0.40 to 1.90 cm2, mean 1.08 +/- 0.37 cm2). There was a moderate correlation between two-dimensional echocardiographic and invasive measurements (r = 0.65, SEE = 0.20 cm2). MOA calculated by the PHT showed only poor correlation with cardiac catheterization (r = 0.38 SEE = 0.37 cm2). We found better correlations for the continuity equation (r = 0.73, SEE = 0.35 cm2) and Doppler-echocardiographic application of the Gorlin formula (r = 0.81, SEe = 0.27 cm2). Doppler-echocardiographic use of the Gorlin formula yielded the best prediction of the severity of mitral valve stenosis (concordance with invasive measurement in 82%).

CONCLUSION

Pressure half-time is only a poor predictor of the severity of mitral valve stenosis. More accurate results are obtained by Doppler-echocardiographic applications of the continuity equation and especially the Gorlin formula.

Biochemical and biological consequences of changing the specificity of p21ras from guanosine to xanthosine nucleotides

The D119N mutation of p21ras was prepared by site-directed mutagenesis. Its nucleotide binding properties were investigated using fluorescently labelled guanosine and xanthosine nucleotides. Its affinity for guanosine nucleotides is severely reduced, with a concomitant increase in the affinity for xanthosine nucleotides, which leads to an almost complete reversal of base specificity. The protein is a GTPase as well as a XTPase and the hydrolysis reaction can be efficiently stimulated by GAP. Dissociation of XDP from the mutant is stimulated by the guanine nucleotide exchange factor Cdc25Mm in a similar manner to that of GDP from wildtype. The interaction of the mutant with the effector domain of c-Raf kinase or Ral-GEF is normal. In microinjection experiments in PC12 and NIH3T3 cells the protein behaves as an oncogenic mutant due to its high dissociation rate for GDP. However, when the protein is loaded with XDP before microinjection the onset of the oncogenic signal can be efficiently retarded. Thus, the protein behaves initially as wildtype and later as an oncogenic protein.

Interaction of guanosine nucleotides and their analogs with elongation factor Tu from Thermus thermophilus

Transient kinetic experiments on the interaction of nucleotide-free EF-Tu from Thermus thermophilus with nucleotides using intrinsic protein fluorescence, extrinsic nucleotide fluorescence and fluorescence resonance energy transfer show that nucleotide binding is in general at least a two-step process. The first step is a weak initial binding, which is followed by a relatively slow isomerization of the protein-nucleotide complex in which changes of both intrinsic and extrinsic fluorescence, as well as energy transfer, occur. The values obtained for the equilibrium and kinetic constants confirm the earlier observation that EF-Tu has a higher affinity for GDP than GTP. This is mainly due to a lower dissociation rate constant for GDP, in combination with a somewhat higher effective association rate constant. Modifications of the triphosphate moiety of GTP are quite well tolerated by EF-Tu, with GTP gamma S displaying the same affinity as GTP and with GppNHp and GppCH2p being only ca. 2-3-fold less strongly bound. Caged GTP is bound about 6-fold more weakly than GTP. These results suggest that the binding of GppNHp and GppCH2p is likely to be similar to that of GTP. The photolytic protecting group of caged GTP (or the loss of one of the negative charges on the gamma-phosphate group) appears to interfere to a certain extent with the interaction with the protein, but the affinity is high enough to permit generation of 1:1 complexes for dynamic structural studies. Discrimination between GDP and ADP is dramatic, with a difference of 6 orders of magnitude in affinity.

Enhancement of glucose disposal in patients with type 2 diabetes by alpha-lipoic acid

Insulin resistance of skeletal muscle glucose uptake is a prominent feature of Type II diabetes (NIDDM); therefore pharmacological interventions should aim to improve insulin sensitivity. Alpha-lipoic acid (CAS 62-46-4, thioctic acid, ALA), a natural occurring compound frequently used for treatment of diabetic polyneuropathy, enhances glucose utilization in various experimental models. To see whether this compound also augments insulin mediated glucose disposal in NIDDM, 13 patients received either ALA (1000 mg/Thioctacid/500 ml NaCl, n = 7) or vehicle only (500 ml NaCl, n = 6) during a glucose-clamp study. Both groups were comparable in age, body-mass index and duration of diabetes and had a similar degree of insulin resistance at baseline. Acute parenteral administration of ALA resulted in a significant increase of insulin-stimulated glucose disposal; metabolic clearance rate (MCR) for glucose rose by about 50% (3.76 ml/kg/min = pre vs. 5.82 ml/kg/min = post, p < 0.05), whereas the control group did not show any significant change (3.57 ml/kg/min = pre vs. 3.91 ml/kg/min = post). This is the first clinical study to show that alpha-lipoic acid increases insulin stimulated glucose disposal in NIDDM. The mode of action of ALA and its potential use as an antihyperglycemic agent require further investigation.

Independence divergence-generated binary trees of amino acids

The discovery of the relationship between amino acids is important in terms of the replacement ability, as used in protein engineering homology studies, and gaining a better understanding of the roles which various properties of the residues play in the creation of a unique, stable, 3-D protein structure. Amino acid sequences of proteins edited by evolution are anything but random. The measure of nonrandomness, i.e. the level of editing, can be characterized by an independence divergence value. This parameter is used to generate binary tree relationships between amino acids. The relationships of residues presented in this paper are based on protein building features and not on the physico-chemical characteristics of amino acids. This approach is not biased by the tautology present in all sequence similarity-based relationship studies. The roles which various physico-chemical characteristics play in the determination of the relationships between amino acids are also discussed.

Substrate and product structural requirements for binding of nucleotides to H-ras p21: the mechanism of discrimination between guanosine and adenosine nucleotides

The interaction of the protein product of the H-ras oncogene with a series of nucleoside di- and triphosphates has been examined to investigate the tolerance of the active site to departures from the GTP or GDP structures. Nucleotides which bind relatively strongly could be used as competitors of GDP in a simple filter binding assay to give semiquantitave estimates of their affinities. For more weakly binding nucleotides or to obtain quantitative data, a transient kinetic method was used which was based on determination of the association and dissociation rate constants. The results obtained indicate that substantial modification of the sugar or phosphate structure is tolerated with little or moderate loss of affinity, but that large losses in affinity occur on modification of the base structure. In particular, replacing the guanine by an adenine residue leads to a dramatic loss of affinity. Thus, discrimination against ATP and ADP is very high (relative affinities of ATP and GTP 1:10(7)). This is due not only to loss of positive (stabilizing) interactions, but especially to the introduction of negative ones.

Chaos game representation of protein structures

Chaos game representation (CGR) was proposed recently to visualize nucleotide sequences as one of the first applications of this technique in the field of biochemistry. In this paper we would like to demonstrate that representations similar to CGR can be generalized and applied for visualizing and analyzing protein databases. Examples of applications will be presented for investigating regularities, and motifs in the primary structure of proteins, and for analyzing possible structural attachments on the super-secondary structure level of proteins. A further application will be presented for testing structure prediction methods using CGR.

New alignment strategy for transmembrane proteins

In this paper an algorithm which locates helical transmembrane segments is described. It is shown that given the location of transmembrane helices of a protein, corresponding helices in another membrane related protein can be pinpointed. The method seems to be extremely insensitive to sequence identity but highly sensitive to the property of a sequence to assume transmembrane helical structure. As an example, using the present method, a sequence alignment between bacteriorhodopsin and human rhodopsin is carried out and it provides a good starting point for homology modeling of this G-protein coupled receptor. It is difficult to obtain this particular alignment using the traditional methods because of poor sequence homology. There are indications that hint at the broader range of applicability of the presented method.

Allelic inactivation regulates olfactory receptor gene expression

We suggest a model in which a hierarchy of controls is exerted on the family of odorant receptor genes to assure that a sensory neuron expresses a single receptor from a family of 1000 genes. We propose that a cis-regulatory element directs the stochastic expression of only one gene from a large array of linked receptor genes. Moreover, only one allelic array encoding multiple receptor genes is active in an individual neuron. We demonstrate that in a neuron expressing a given receptor, expression derives exclusively from one allele. In addition, we observe that alleles encoding the odorant receptors are replicated asynchronously, a phenomenon consistently associated with allelic inactivation. This model, involving inactivation of one allelic array and cis control of the active array, provides a mechanism such that individual neurons express one or a small number of receptors.

Different sequence environments of amino acid residues involved and not involved in long-range interactions in proteins

No method has yet been available to decode information, hidden in the protein primary structure, on long-range interactions of amino acids. Even a limited amount of information on long-range interactions could help in conformational energy calculations of protein structures and could lead to a better understanding of how the primary structure of proteins determines their conformation. The sequence environments of amino-acid residues were compared from the viewpoint of their participation in long-range interactions. By using the simplest definition, residues were considered as partners in a long-range interaction if they were at least 20 residues apart in the sequence and their C alpha distance was less than 7 A. In spite of this rather crude definition, an analysis of 88 unrelated proteins has shown that the sequence environments (10 residues on each side) of those amino acids which are involved in long-range interactions and of those which are not are significantly different according to the criteria of mathematical statistics. Moreover, in many cases the differences are so pronounced that the involvement of a given amino acid in long-range interactions can be predicted from its sequence environment.

Predictions from the regularities of the primary structure of proteins

Statistical analysis of large data sets indicates the existence of short-range regularities in the primary structure of proteins. In this paper the range and measure of these short-range regularities and various prediction methods based on them are discussed. The methods include predictions for domain boundaries of multidomain proteins; sizes of low-energy building blocks used in the calculation of protein structure as an assembly of stable overlapping segments; replaceability of amino acids; cis and trans conformation of proline residues; disulfide-forming Cys residues; surface exposure of amino acids; and tyrosine sulfation sites in proteins.

Allele-specific replication timing of imprinted gene regions

Several lines of evidence suggest that the paternal and maternal genomes may have different expression patterns in the developing organism and this has been confirmed by the identification of endogenous genes that are parentally imprinted in the mouse. Little is known about the precise mechanisms involved in the process, but structural differences between the two alleles must somehow provide cis-acting signals for directing parental-specific transcription. Cell-cycle replication time is one parameter that has been shown to be associated with both tissue-specific gene expression and the allele-specific transcription patterns of the X chromosomes in female cells. For this reason we have examined the replication timing patterns for the chromosomal regions containing the imprinted genes Igf2, Igf2r, H19 and Snrpn in the mouse. At all of these sites, and their corresponding positions in the human genome, the two homologous alleles replicate asynchronously and it is always the paternal allele that is early-replicating. Thus imprinted genes appear to be embedded in large DNA domains with differential replication patterns, which may provide a structural imprint for parental identity.

[Multicenter prospective study of cardiac accidents during treatments with 5-FU]

In a prospective, multicenter study, we evaluated the incidence of adverse cardiac effects in 1097 patients receiving 5-FU as a short i.v. perfusion or as a continuous perfusion over 3 to 5 days. There were 29 cardiac events (incidence 1.6%; 4.5% in patients with a history of cardiovascular disease, 1.1% in the remainder). Adverse effects were more frequent in the patients with advanced WHO (WHO = OMS) stage (2 or 3) primary tumors of the upper respiratory or digestive tract, or of the gastrointestinal tract, when 5-FU was given as a continuous perfusion. They also appeared to be more frequent in patients with a history of cardiovascular disease, and mainly occurred during the second or third day of the first course of treatment. Retreatment of eight patients with 5-FU led to the recurrence of symptoms in five. The outcome of these adverse cardiac effects was generally favorable, but 11.5% of the patients died.

Different sequence environments of cysteines and half cystines in proteins. Application to predict disulfide forming residues

Protein sequences are often derived by translating genetic information, rather than by classical protein sequencing. At the DNA level cysteines and half cystines are indistinguishable. Here we show that the sequential environments of 'free' cysteine and half cystine are different. A possible origin of this difference is discussed and a simple method to predict cysteines and half cystines from the amino acid sequence is also presented.

Identification of the cytochrome P450 IIIA family as the enzymes involved in the N-demethylation of tamoxifen in human liver microsomes

The antiestrogen tamoxifen (Tam or Nolvadex, ICI)-Z-1-[4-[2-(dimethylamino) ethoxy]phenyl]-1,2-diphenyl-1-butene is widely used in treatment of hormone-dependent breast cancer. The drug is extensively metabolized by cytochrome P450 dependent hepatic mixed function oxidase in man, yielding mainly the N-desmethyl metabolite (DMT). This study has been carried out to determine the P450 enzyme involved in the N-oxidative demethylation of Tam in microsomal samples from 25 human livers (23 adults, two children). This metabolic step was inhibited by carbon monoxide up to 75%. Tam was demethylated into DMT with an apparent Km of 98 +/- 10 microM; rates varied between 37 and 446 pmol/min/mg microsomal protein. These metabolic rates were strongly correlated with 6 beta-hydroxylation of testosterone (r = 0.83) and erythromycin N-demethylase (r = 0.75), both activities known to be associated with P450 IIIA enzyme. To further assess whether or not the Tam demethylation pathway is catalysed by the same P450, the inhibitory effect of TST on this reaction was determined. The competitive inhibition had an apparent Ki of 100 +/- 10 microM. Drugs such as erythromycin, cyclosporin, nifedipine and diltiazem were shown to inhibit in vitro the metabolism of tamoxifen. Furthermore the P450 IIIA content of liver microsomal samples, measured by Western blot technique using a monoclonal P450NF (nifedipine) antibody, was strongly correlated with DMT formation (r = 0.87). Tam N-demethylase activity was inhibited by more than 65% with polyclonal anti-human anti-P450NF. All these in vitro observations establish that a P450 enzyme of the IIIA sub-family is involved in the oxidative demethylation of tamoxifen in human liver.

Calculation of protein conformation as an assembly of stable overlapping segments: application to bovine pancreatic trypsin inhibitor

Conformations of bovine pancreatic trypsin inhibitor were calculated by assuming that the final structure as well as properly chosen overlapping segments thereof are simultaneously in low-energy (not necessarily the lowest-energy) conformational states. Therefore, the whole chain can be built up from building blocks whose conformations are determined primarily by short-range interactions. Our earlier buildup procedure was modified by taking account of a statistical analysis of known amino acid sequences that indicates that there is nonrandom pairing of amino acid residues in short segments along the chain, and by carrying out energy minimization on only these segments and on the whole chain [without minimizing the energies of intermediate-size segments (20-30 residues long)]. Results of this statistical analysis were used to determine the variable sizes of the overlapping oligopeptide building blocks used in the calculations; these varied from tripeptides to octapeptides, depending on the amino acid sequence. Successive stages of approximations were used to combine the low-energy conformations of these building blocks in order to keep the number of variables in the computations to a manageable size. The calculations led to a limited number of conformations of the protein (only two different groups, with very similar structure within each group), most residues of which were in the same conformational state as in the native structure.

Predicting isomorphic residue replacements for protein design

The replaceability of amino acids as reflected in their neighbourhood selectivity is analyzed in this paper. Neighbourhood selectivity was found to be more characteristic of the individual amino acids than the other commonly used parameters. The residue replacement rank obtained was compared with other proposed ranks and was tested on naturally accepted point mutations in homologous proteins.