Computational approaches to shed light on molecular mechanisms in biological processes

Computational approaches based on Molecular Dynamics simulations, Quantum Mechanical methods and 3D Quantitative Structure-Activity Relationships were employed by computational chemistry groups at the University of Milano-Bicocca to study biological processes at the molecular level. The paper reports the methodologies adopted and the results obtained on Aryl hydrocarbon Receptor and homologous PAS proteins mechanisms, the properties of prion protein peptides, the reaction pathway of hydrogenase and peroxidase enzymes and the defibrillogenic activity of tetracyclines. © Springer-Verlag 2007

Molecular dynamics ensemble refinement of the heterogeneous native state of NCBD using chemical shifts and NOEs

Many proteins display complex dynamical properties that are often intimately linked to their biological functions. As the native state of a protein is best described as an ensemble of conformations, it is important to be able to generate models of native state ensembles with high accuracy. Due to limitations in sampling efficiency and force field accuracy it is, however, challenging to obtain accurate ensembles of protein conformations by the use of molecular simulations alone. Here we show that dynamic ensemble refinement, which combines an accurate atomistic force field with commonly available nuclear magnetic resonance (NMR) chemical shifts and NOEs, can provide a detailed and accurate description of the conformational ensemble of the native state of a highly dynamic protein. As both NOEs and chemical shifts are averaged on timescales up to milliseconds, the resulting ensembles reflect the structural heterogeneity that goes beyond that probed, e.g., by NMR relaxation order parameters. We selected the small protein domain NCBD as object of our study since this protein, which has been characterized experimentally in substantial detail, displays a rich and complex dynamical behaviour. In particular, the protein has been described as having a molten-globule like structure, but with a relatively rigid core. Our approach allowed us to describe the conformational dynamics of NCBD in solution, and to probe the structural heterogeneity resulting from both short- and long-timescale dynamics by the calculation of order parameters on different time scales. These results illustrate the usefulness of our approach since they show that NCBD is rather rigid on the nanosecond timescale, but interconverts within a broader ensemble on longer timescales, thus enabling the derivation of a coherent set of conclusions from various NMR experiments on this protein, which could otherwise appear in contradiction with each other

Seismic tomography of the North Anatolian Fault: New insights into structural heterogeneity along a continental strike-slip fault

Knowledge of the structure of continental strike-slip faults within the lithosphere is essential to understand where the deformation occurs and how strain localizes with depth. With the aim to improve the constraints on the lower crust and upper mantle structure of a major continental strike-slip fault, we present a high-resolution teleseismic tomography of the North Anatolian Fault Zone (NAFZ) in Turkey. Our results highlight the presence of a relatively high velocity body between the two branches of the fault and significant along-strike variations in the NAFZ velocity structure over distances of ~20 km. We interpret these findings as evidence of laterally variable strain focussing caused by preexisting heterogeneity. Low velocities observed in the crust and upper mantle beneath the NAFZ support the presence of a narrow shear zone widening in the upper mantle, where we constrain its width to be ~50 km.Major funding was provided by the UK Natural Environment Research Council (NERC) under grant NE/I028017/1. Equipment was provided and supported by the NERC Geophysical Equipment Facility (SEIS-UK). This project is also supported by Bogaziçi University Scientific ˘ Research Projects (BAP) under grant 6922 and Turkish State Planning Organization (DPT) under the TAM project, number 2007K120610

Effect of vitamin D supplementation on assisted reproduction technology (ART) outcomes and underlying biological mechanisms: protocol of a randomized clinical controlled trial. The "supplementation of vitamin D and reproductive outcome" (SUNDRO) study

Background Vitamin D plays an important role in human physiology and pathology. The receptor for vitamin D regulates 0.5-5% of the human genome. Accordingly, vitamin D insufficiency has been shown to increase the risk of several diseases. In recent years, based on growing evidence, on a role of vitamin D has been also postulated in reproductive health both in animals and humans, especially in female fertility female fertility. In vitro fertilization success was shown to be higher in women with appropriate reserves of vitamin D. However a causal relation has not been demonstrated and randomized controlled trials testing the effectiveness of vitamin D supplementation in IVF are warranted. Methods This is a multicenter randomized double blinded placebo controlled study aimed at determining the benefits of vitamin D [25(OH)D] supplementation in improving clinical pregnancy rate in women undergoing IVF. Eligible women with a serum level of 25-hydroxyvitamin D [25(OH)D] < 30 ng/ml will be randomized. Recruited women will be given the drug (either 600,000 IU of 25(OH) D or placebo in a single oral administration) at the time of randomization. Two centres will participate and the sample size (700 women) is foreseen to be equally distributed between the two. Patients will be treated according to standard IVF protocols. Discussion The primary aim of the study is the cumulative clinical pregnancy rate per oocyte retrieval. Clinical pregnancy is defined as the presence of at least one intrauterine gestational sac with viable foetus at first ultrasound assessment (3 weeks after a positive human chorionic gonadotropin [hCG] assessment). Secondary outcomes include: 1) clinical and embryological variables; 2) oocyte and endometrium quality at a molecular level. To investigate this latter aspect, samples of cumulus cells, follicular and endometrial fluids will be obtained from a subgroup of 50 age-matched good-prognosis cases and controls

Prediction of age at menopause from assessment of ovarian reserve may be improved by using body mass index and smoking status.

OBJECTIVE: Menopause is the consequence of exhaustion of the ovarian follicular pool. AMH, an indirect hormonal marker of ovarian reserve, has been recently proposed as a predictor for age at menopause. Since BMI and smoking status are relevant independent factors associated with age at menopause we evaluated whether a model including all three of these variables could improve AMH-based prediction of age at menopause. METHODS: In the present cohort study, participants were 375 eumenorrheic women aged 19-44 years and a sample of 2,635 Italian menopausal women. AMH values were obtained from the eumenorrheic women. RESULTS: Regression analysis of the AMH data showed that a quadratic function of age provided a good description of these data plotted on a logarithmic scale, with a distribution of residual deviates that was not normal but showed significant left-skewness. Under the hypothesis that menopause can be predicted by AMH dropping below a critical threshold, a model predicting menopausal age was constructed from the AMH regression model and applied to the data on menopause. With the AMH threshold dependent on the covariates BMI and smoking status, the effects of these covariates were shown to be highly significant. CONCLUSIONS: In the present study we confirmed the good level of conformity between the distributions of observed and AMH-predicted ages at menopause, and showed that using BMI and smoking status as additional variables improves AMH-based prediction of age at menopause

Vitamin D deficiency and infertility : insights from in vitro fertilization cycles

Context: Vitamin D deficiency has been proven to affect fertility in mammals, but data in human is less convincing. In particular, data on in vitro fertilization (IVF), an attractive model to draw information on this topic, are sparse and conflicting.Objective: Our objective was to investigate IVF outcome in women with deficient 25-hydroxyvitamin D [25 (OH)D] serum levels (30 ng/mL) had the highest chances of pregnancy.Conclusions: VitaminDis an emerging factor influencing female fertility and IVF outcome. Additional studies are pressingly needed to confirm a causal relationship and to investigate the potential therapeutic benefits of vitamin D supplementation

Uterine artery Doppler pulsatility index at 11-38 weeks in ICSI pregnancies with egg donation

BACKGROUND: Uterine artery Doppler pulsatility index (UtA-PI) may be different in pregnancies with egg donation (ICSI-ED) as compared to conceptions with autologous intra-cytoplasmatic sperm injection (autologous ICSI) and to spontaneous conceptions (SC). METHODS: One hundred and ninety-four pregnant women with different modes of conception (MC) were prospectively evaluated: 53 ICSI-ED, 36 autologous ICSI and 105 SC. To evaluate the effects of different MC on PI, multivariable linear regression (MLR) models predicting UtA-PI were fitted after adjustment for maternal age, body mass index, race, parity, smoking status and gestational age. RESULTS: In the first trimester, at MLR, autologous ICSI was not associated with a significantly different UtA-PI [estimate (EST) 0.01; 95% confidence interval (CI) -0.19, 0.2; P=0.9] when compared to SC. Conversely, MC by ICSI-ED was associated with lower first trimester UtA-PI (EST -0.32; CI -0.55, -0.08; P=0.01) when compared to SC. At MLR, MC by autologous ICSI and by ICSI-ED were not associated with significant differences in the second and third trimester UtA-PI when compared to SC. CONCLUSION: ICSI-ED conception presented lower UtA-PI when compared to SC at 11+0-13+6 weeks but not at later assessments. Correction of UtA-PI measurement specifying the origin of oocyte may be useful in first trimester screening

DNA-binding protects p53 from interactions with cofactors involved in transcription-independent functions

Binding-induced conformational changes of a protein at regions distant from the binding site may play crucial roles in protein function and regulation. The p53 tumour suppressor is an example of such an allosterically regulated protein. Little is known, however, about how DNA binding can affect distal sites for transcription factors. Furthermore, the molecular details of how a local perturbation is transmitted through a protein structure are generally elusive and occur on timescales hard to explore by simulations. Thus, we employed state-of-the-art enhanced sampling atomistic simulations to unveil DNA-induced effects on p53 structure and dynamics that modulate the recruitment of cofactors and the impact of phosphorylation at Ser215. We show that DNA interaction promotes a conformational change in a region 3 nm away from the DNA binding site. Specifically, binding to DNA increases the population of an occluded minor state at this distal site by more than 4-fold, whereas phosphorylation traps the protein in its major state. In the minor conformation, the interface of p53 that binds biological partners related to p53 transcription-independent functions is not accessible. Significantly, our study reveals a mechanism of DNA-mediated protection of p53 from interactions with partners involved in the p53 transcription-independent signalling. This also suggests that conformational dynamics is tightly related to p53 signalling

Risk of miscarriage in women with endometriosis: insights from in vitro fertilization cycles

Objective: To evaluate whether women with endometriosis achieving singleton pregnancies with IVF face an increased risk of miscarriage. Design: Matched case-control study. Setting: Infertility units. Patient(s): Women achieving singleton pregnancies with the use of IVF were considered. Cases were women with a history of surgery for endometriosis and those who were documented the presence of ovarian endometriomas at the time of the IVF cycle (n = 313). Controls were matched to cases by age (\ub16 months), type of cycle (fresh or frozen cycle). and study period (n = 313). Intervention(s): Retrospective review of women undergoing IVF. Main Outcome Measure(s): Rate of miscarriage before 12 weeks' gestation. Result(s): The number of miscarriages in women with and without endometriosis was similar, being 48 (15%) and 60 (19%), respectively. The odds ratio of miscarriage in affected women was 0.76 (95% confidence interval 0.50-1.16). The odds ratio adjusted for body mass index (BMI), parity, duration of infertility, and male factor infertility was 0.81 (95% confidence interval 0.53-1.25). Subgroup analyses according to the type of cycle, the number of embryos transferred, the presence of endometriomas, and the history of surgery for endometriosis did not document any subgroup at significant increased risk of miscarriage. Conclusion(s): The risk of miscarriage is not increased in women with endometriosis achieving pregnancy with the use of IVF