Free-Energy Calculations Highlight Differences in Accuracy between X-Ray and NMR Structures and Add Value to Protein Structure Prediction

AbstractBackground: While X-ray crystallography structures of proteins are considerably more reliable than those from NMR spectroscopy, it has been difficult to assess the inherent accuracy of NMR structures, particularly the side chains.Results: For 15 small single-domain proteins, we used a molecular mechanics-/dynamics-based free-energy approach to investigate native, decoy, and fully extended alpha conformations. Decoys were all less energetically favorable than native conformations in nine of the ten X-ray structures and in none of the five NMR structures, but short 150 ps molecular dynamics simulations on the experimental structures caused them to have the lowest predicted free energy in all 15 proteins. In addition, a strong correlation exists (r2 = 0.86) between the predicted free energy of unfolding, from native to fully extended conformations, and the number of residues.Conclusions: This work suggests that the approximate treatment of solvent used in solving NMR structures can lead NMR model conformations to be less reliable than crystal structures. This conclusion was reached because of the considerably higher calculated free energies and the extent of structural deviation during aqueous dynamics simulations of NMR models compared to those determined by X-ray crystallography. Also, the strong correlation found between protein length and predicted free energy of unfolding in this work suggests, for the first time, that a free-energy function can allow for identification of the native state based on calculations on an extended state and in the absence of an experimental structure

Free energies of binding of R- and S-propranolol to wild-type and F483A mutant cytochrome P450 2D6 from molecular dynamics simulations

Detailed molecular dynamics (MD) simulations have been performed to reproduce and rationalize the experimental finding that the F483A mutant of CYP2D6 has lower affinity for R-propranolol than for S-propranolol. Wild-type (WT) CYP2D6 does not show this stereospecificity. Four different approaches to calculate the free energy differences have been investigated and were compared to the experimental binding data. From the differences between calculations based on forward and backward processes and the closure of thermodynamic cycles, it was clear that not all simulations converged sufficiently. The approach that calculates the free energies of exchanging R-propranolol with S-propranolol in the F483A mutant relative to the exchange free energy in WT CYP2D6 accurately reproduced the experimental binding data. Careful inspection of the end-points of the MD simulations involved in this approach, allowed for a molecular interpretation of the observed differences

Molecular dynamics simulations and in silico peptide ligand screening of the Elk-1 ETS domain

Background: The Elk-1 transcription factor is a member of a group of proteins called ternary complex factors, which serve as a paradigm for gene regulation in response to extracellular signals. Its deregulation has been linked to multiple human diseases including the development of tumours. The work herein aims to inform the design of potential peptidomimetic compounds that can inhibit the formation of the Elk-1 dimer, which is key to Elk-1 stability. We have conducted molecular dynamics simulations of the Elk-1 ETS domain followed by virtual screening. Results: We show the ETS dimerisation site undergoes conformational reorganisation at the a1b1 loop. Through exhaustive screening of di- and tri-peptide libraries against a collection of ETS domain conformations representing the dynamics of the loop, we identified a series of potential binders for the Elk-1 dimer interface. The di-peptides showed no particular preference toward the binding site; however, the tri-peptides made specific interactions with residues: Glu17, Gln18 and Arg49 that are pivotal to the dimer interface. Conclusions: We have shown molecular dynamics simulations can be combined with virtual peptide screening to obtain an exhaustive docking protocol that incorporates dynamic fluctuations in a receptor. Based on our findings, we suggest experimental binding studies to be performed on the 12 SILE ranked tri-peptides as possible compounds for the design of inhibitors of Elk-1 dimerisation. It would also be reasonable to consider the score ranked tri-peptides as a comparative test to establish whether peptide size is a determinant factor of binding to the ETS domain

Continuous glucose monitoring in pregnant women with type 1 diabetes (CONCEPTT): a multicentre international randomised controlled trial.

BACKGROUND: Pregnant women with type 1 diabetes are a high-risk population who are recommended to strive for optimal glucose control, but neonatal outcomes attributed to maternal hyperglycaemia remain suboptimal. Our aim was to examine the effectiveness of continuous glucose monitoring (CGM) on maternal glucose control and obstetric and neonatal health outcomes. METHODS: In this multicentre, open-label, randomised controlled trial, we recruited women aged 18-40 years with type 1 diabetes for a minimum of 12 months who were receiving intensive insulin therapy. Participants were pregnant (≤13 weeks and 6 days' gestation) or planning pregnancy from 31 hospitals in Canada, England, Scotland, Spain, Italy, Ireland, and the USA. We ran two trials in parallel for pregnant participants and for participants planning pregnancy. In both trials, participants were randomly assigned to either CGM in addition to capillary glucose monitoring or capillary glucose monitoring alone. Randomisation was stratified by insulin delivery (pump or injections) and baseline glycated haemoglobin (HbA1c). The primary outcome was change in HbA1c from randomisation to 34 weeks' gestation in pregnant women and to 24 weeks or conception in women planning pregnancy, and was assessed in all randomised participants with baseline assessments. Secondary outcomes included obstetric and neonatal health outcomes, assessed with all available data without imputation. This trial is registered with ClinicalTrials.gov, number NCT01788527. FINDINGS: Between March 25, 2013, and March 22, 2016, we randomly assigned 325 women (215 pregnant, 110 planning pregnancy) to capillary glucose monitoring with CGM (108 pregnant and 53 planning pregnancy) or without (107 pregnant and 57 planning pregnancy). We found a small difference in HbA1c in pregnant women using CGM (mean difference -0·19%; 95% CI -0·34 to -0·03; p=0·0207). Pregnant CGM users spent more time in target (68% vs 61%; p=0·0034) and less time hyperglycaemic (27% vs 32%; p=0·0279) than did pregnant control participants, with comparable severe hypoglycaemia episodes (18 CGM and 21 control) and time spent hypoglycaemic (3% vs 4%; p=0·10). Neonatal health outcomes were significantly improved, with lower incidence of large for gestational age (odds ratio 0·51, 95% CI 0·28 to 0·90; p=0·0210), fewer neonatal intensive care admissions lasting more than 24 h (0·48; 0·26 to 0·86; p=0·0157), fewer incidences of neonatal hypoglycaemia (0·45; 0·22 to 0·89; p=0·0250), and 1-day shorter length of hospital stay (p=0·0091). We found no apparent benefit of CGM in women planning pregnancy. Adverse events occurred in 51 (48%) of CGM participants and 43 (40%) of control participants in the pregnancy trial, and in 12 (27%) of CGM participants and 21 (37%) of control participants in the planning pregnancy trial. Serious adverse events occurred in 13 (6%) participants in the pregnancy trial (eight [7%] CGM, five [5%] control) and in three (3%) participants in the planning pregnancy trial (two [4%] CGM and one [2%] control). The most common adverse events were skin reactions occurring in 49 (48%) of 103 CGM participants and eight (8%) of 104 control participants during pregnancy and in 23 (44%) of 52 CGM participants and five (9%) of 57 control participants in the planning pregnancy trial. The most common serious adverse events were gastrointestinal (nausea and vomiting in four participants during pregnancy and three participants planning pregnancy). INTERPRETATION: Use of CGM during pregnancy in patients with type 1 diabetes is associated with improved neonatal outcomes, which are likely to be attributed to reduced exposure to maternal hyperglycaemia. CGM should be offered to all pregnant women with type 1 diabetes using intensive insulin therapy. This study is the first to indicate potential for improvements in non-glycaemic health outcomes from CGM use. FUNDING: Juvenile Diabetes Research Foundation, Canadian Clinical Trials Network, and National Institute for Health Research

The case for a New Frontiers-class Uranus Orbiter:System science at an underexplored and unique world with a mid-scale mission

Current knowledge of the Uranian system is limited to observations from the flyby of Voyager 2 and limited remote observations. However, Uranus remains a highly compelling scientific target due to the unique properties of many aspects of the planet itself and its system. Future exploration of Uranus must focus on cross-disciplinary science that spans the range of research areas from the planet's interior, atmosphere, and magnetosphere to the its rings and satellites, as well as the interactions between them. Detailed study of Uranus by an orbiter is crucial not only for valuable insights into the formation and evolution of our solar system but also for providing ground truths for the understanding of exoplanets. As such, exploration of Uranus will not only enhance our understanding of the ice giant planets themselves but also extend to planetary dynamics throughout our solar system and beyond. The timeliness of exploring Uranus is great, as the community hopes to return in time to image unseen portions of the satellites and magnetospheric configurations. This urgency motivates evaluation of what science can be achieved with a lower-cost, potentially faster-turnaround mission, such as a New Frontiers–class orbiter mission. This paper outlines the scientific case for and the technological and design considerations that must be addressed by future studies to enable a New Frontiers–class Uranus orbiter with balanced cross-disciplinary science objectives. In particular, studies that trade scientific scope and instrumentation and operational capabilities against simpler and cheaper options must be fundamental to the mission formulation

Monetary Policy in an Estimated Open-Economy Model with Imperfect Pass-Through

We develop a structural model of a small open economy with gradual exchange rate pass-through and endogenous inertia in inflation and output. We then estimate the model by matching the implied impulse responses with those obtained from a VAR model estimated on Swedish data. Although our model is highly stylized it captures very well the responses of output, domestic and imported inflation, the interest rate, and the real exchange rate. However, in order to account for the observed persistence in the real exchange rate and the large deviations from UIP, we need a large and volatile premium on foreign exchange

Solvation Free Energies of Amides and Amines: Disagreement between Free Energy Calculations and Experiment

We present molecular dynamidfree energy calculations on the molecules acetamide, N-methylacetamide, N,N-dimethylacetamide, ammonia, methylamine, dimethylamine, and trimethylamine. Unlike the experimental data, which suggest a very non-additive solvation free energy (N-methylacetamide and methylamine having the most negative free energy of solvation), the calculations all find that the free energy of solvation monotonically increases as a function of methyl addition. The disagreement with experiment is surprising, given the very good agreement (within 0.5 kcaYmo1) with experiment for calculation of the solvation free energy of methane, ethane, propane, water, methanol, and dimethyl ether