Structural analysis of intrinsically disordered proteins: computer atomistic simulation

Intrinsically disordered proteins (IDPs) are biomolecules that do not have a definite 3D structure; their role in the biochemical network of a cell relates to their ability to switch rapidly among different secondary and tertiary structures. For this reason, applying a simulation computer program to their structural study turns out to be problematic, as their dynamical simulation cannot start from a known list of atomistic positions, as is the case for globular proteins that do crystallize and that one can analyse by X-ray spectroscopy to determine their structure. We have established a method to perform a computer simulation of these proteins, apt to gather statistically significant data on their transient structures. The only required input to start the procedure is the primary sequence of the disordered domains of the protein, and the 3D structure of the ordered domains, if any. For a fully disordered protein the method is as follows: (a) The first step is the creation of a multi-rod-like configuration of the molecule, derived from its primary sequence. This structure evolves dynamically in vacuo or in an implicit model of solvent, until its gyration radius - or any other measure of the overall configuration of the molecule - reaches the experimental average value; at this point, one may follow two different paths. (b1) If the study focuses on transient secondary structures of the molecule, one puts the structure obtained at the end of the first step in a box containing solvent molecules in explicit implementation, and a standard molecular dynamics simulation follows. (b2) If the study focuses on the tertiary structure of the molecule, a larger sampling of the phase space is required, with the molecule moving in very large and diverse regions of the phase space. To this end, the structure of the IDP is let evolve dynamically in an implicit solvent using metadynamics, an algorithm that keeps track of the regions of the phase space already sampled, and forces the system to wander in further regions of the phase space. (c) One can increase the accuracy of the statistical information gathered in both cases by fitting, where available, experimental data of the protein. In this step one extracts an ensemble of ’best’ conformers from the pool of all configurations produced in the simulated dynamics. One derives this ensemble by means of an ensemble optimization method, implementing a genetic algorithm. We have applied this procedure to the simulation of tau, one of the largest fully disordered proteins, which is involved in the development of Alzheimer’s disease and of other neurodegenerative diseases. We have combined the results of our simulation with small-angle X-ray scattering experimental data to extract from the dynamics an optimized ensemble of most probable conformers of tau. The method can be easily adapted to IDPs entailing ordered domains

Optimal revascularization in diabetes after the FREEDOM trial: Were the controversies finally settled?

The prevalence of diabetes mellitus (DM) is growing worldwide. Prothrombotic and proinfl ammatorystates, in adjunct to endothelial dysfunction and metabolic disorders, such as hyperglycemia,dyslipidemia, obesity, insulin resistance, and oxidative stress, are key features of theaccelerated atherosclerotic progression observed in patients with DM. Moreover, drug-elutingstents (DES) thrombosis rate was higher in DM than in non-DM patients and DM itself wasidentifi ed as an independent predictor of stent thrombosis, particularly due to the impairedresponse to dual antiplatelet therapy. The accumulating data even before the FREEDOM trialprovided strong evidence that in patients with DM and complex coronary artery disease, coronaryartery bypass grafting (CABG) was superior to percutaneous coronary intervention (PCI)which was based on the fi rst-generation DES. The FREEDOM trial enrolled 1900 patientswith DM and multivessel coronary artery disease treated with CABG surgery or PCI with thefi rst-generation DES. The patients were followed for a median 3.8 years; CABG was superiorto PCI as it signifi cantly reduced rates of death and myocardial infarction (MI), with a higherrate of stroke. The benefi t of CABG was driven by differences in rates of both MI (p < 0.001)and death from any cause (p = 0.049). Following the FREEDOM results, patients with DMought to be informed before coronary angiography about the potential survival benefi t fromCABG for the treatment of a complex disease. However, it should be noticed that the second generationDES were associated with better outcomes compared to the fi rst-generation DES. Newstent designs are continually being developed, with the aim of further improving the clinicaleffi cacy and the safety profi le of these devices. Therefore, although the results of the FREEDOMtrial clearly demonstrated that CABG was superior to PCI in DM, a comparative analysis ofthe new incoming stents warrants further investigation

A cardiologic approach to non-insulin antidiabetic pharmacotherapy in patients with heart disease

Classical non-insulin antihyperglycemic drugs currently approved for the treatment of type 2 diabetes mellitus (T2DM) comprise five groups: biguanides, sulfonylureas, meglitinides, glitazones and alpha-glucosidase inhibitors. Novel compounds are represented by the incretin mimetic drugs like glucagon like peptide-1 (GLP-1), the dipeptidyl peptidase 4 (DPP-4) inhibitors, dual peroxisome proliferator-activated receptors (PPAR) agonists (glitazars) and amylin mimetic drugs. We review the cardiovascular effects of these drugs in an attempt to improve knowledge regarding their potential risks when treating T2DM in cardiac patients. Metformin may lead to lethal lactic acidosis, especially in patients with clinical conditions that predispose to this complication, such as recent myocardial infarction, heart or renal failure. Sulfonylureas exert their effect by closing the ATP-dependent potassium channels. This prevents the opening of these channels during myocardial ischemia, impeding the necessary hyperpolarization that protects the cell. The combined sulfonylurea/metformin therapy reveals additive effects on mortality in patients with coronary artery disease (CAD). Meglitinides effects are similar to those of sulfonylureas, due to their almost analogous mechanism of action. Glitazones lower leptin levels, leading to weight gain and are unsafe in NYHA class III or IV. The long-term effects of alpha-glucosidase inhibitors on morbidity and mortality rates is yet unknown. The incretin GLP-1 is associated with reductions in body weight and appears to present positive inotropic effects. DPP-4 inhibitors influences on the cardiovascular system seem to be neutral and patients do not gain weight. The future of glitazars is presently uncertain following concerns about their safety. The amylin mimetic drug paramlintide, while a satisfactory adjuvant medication in insulin-dependent diabetes, is unlikely to play a major role in the management of T2DM

Which is the best lipid-modifying strategy in metabolic syndrome and diabetes: fibrates, statins or both?

Although less clinical intervention studies have been performed with fibrates than with statins, there are evidences indicating that fibrates may reduce risk of cardiovascular events. The potential clinical benefit of the fenofibrate will be specified by the ongoing Fenofibrate Intervention and Event Lowering in Diabetes (FIELD) study, which rationale, methods and aims have been just published. Controlled clinical trials show similar or even greater cardiovascular benefits from statins-based therapy in patient subgroups with diabetes compared with overall study populations. Therefore, statins are the drug of first choice for aggressive lipid lowering actions and reducing risk of coronary artery disease in these patients. However, current therapeutic use of statins as monotherapy is still leaving many patients with mixed atherogenic dyslipidemia at high risk for coronary events. A combination statin/fibrate therapy may be often necessary to control all lipid abnormalities in patients with metabolic syndrome and diabetes adequately, since fibrates provide additional important benefits, particularly on triglyceride and HDL-cholesterol levels. Thus, this combined therapy concentrates on all the components of the mixed dyslipidemia that often occurs in persons with diabetes or metabolic syndrome, and may be expected to reduce cardiovascular morbidity and mortality. Safety concerns about some fibrates such as gemfibrozil may lead to exaggerate precautions regarding fibrate administration and therefore diminish the use of the seagents. However, other fibrates, such as bezafibrate and fenofibrate appear to be safer and better tolerated. We believe that a proper co-administration of statins and fibrates, selected on basis of their safety, could be more effective in achieving a comprehensive lipid control as compared with monotherapy

Statistical Laws Governing Fluctuations in Word Use from Word Birth to Word Death

How often a given word is used, relative to other words, can convey information about the word’s linguistic utility. Using Google word data for 3 languages over the 209-year period 1800–2008, we found by analyzing word use an anomalous recent change in the birth and death rates of words, which indicates a shift towards increased levels of competition between words as a result of new standardization technology. We demonstrate unexpected analogies between the growth dynamics of word use and the growth dynamics of economic institutions. Our results support the intriguing concept that a language’s lexicon is a generic arena for competition which evolves according to selection laws that are related to social, technological, and political trends. Specifically, the aggregate properties of language show pronounced differences during periods of world conflict, e.g. World War II

The metabolic syndrome entanglement: Cutting the Gordian knot

Questions have been raised on the clinical value of the metabolic syndrome (MS). The negative opinion regarding MS is anchored basically on a separate analysis of 4 conditions: obesity, dyslipidemia, hypertension and glucose intolerance. The common denominator of these 4 sets of arguments is that they represent an utterly simplistic view of MS as a solely predictive tool of morbidity or mortality. We believe that it is inequitable to compare it with statistically constructed predictive tools, including stronger prognostic variables even unrelated to one another from the biological point of view. Several recent large meta-analyses — one of them including nearly one million patients — systematically showed that people with MS are at increased risk of cardiovascular (CV) events. MS was associated with a 2-fold increase in CV outcomes and a 1.5-fold increase in all-cause mortality rates. A very important finding was that CV risk still remained high in patients with MS but without diabetes. The presence of MS possesses a definitely predictive value, but above all it is a widely accepted concept regarding a biological condition based on complex and interrelated pathophysiological mechanisms emanating from excess central adiposity and insulin resistance. The risk factors are multiplicative, meaning that the risk of a CV disease from risk factors rises geometrically, not linearly, as the number of risk factors increases. Therefore, currently available evidences strongly support the concept of the MS as a critical clustering of CV risk factors and diabetes, representing a true and solid evolving clinical entity

"If it ain't broke, don't fix it": a commentary on the positive-negative results of the ACCORD Lipid study

Even using intensive statin monotherapy, many patients fail to achieve all the desired lipid goals and remain at high residual risk of cardiovascular events. In view of the still unproven decisively intensive "statin as monotherapy" strategy and "residual risk" concept, it is logical to ask whether other strategies, particularly fibrate/statin combination therapy, could be more beneficial and safer. A clear benefit of fibrate monotherapy did emerge previously among patients with atherogenic dyslipidemia (particularly high triglycerides and low high density lipoprotein cholesterol [HDL-C]) typically present in the metabolic syndrome and type 2 diabetes. In contrast, in patients without atherogenic dyslipidemia this favorable effect was not demonstrated

"The metabolic syndrome... is dead": These reports are an exaggeration

The debates continue over the validity of the metabolic syndrome concept. The continuous increment of the obesity pandemic is almost worldwide paralleled by rising rates of metabolic syndrome prevalence. Then, it seems obvious that these debates drove the need for further investigations as well as a deeper cooperation between relevant national and international organizations regarding the issue. Instead, part of the scientific community elected to totally "dismiss" the concept of the metabolic syndrome. Meanwhile, the best available evidence from three consecutive large meta-analyses has systematically shown that people with metabolic syndrome are at increased risk of cardiovascular events. The most recent and largest of them included near one million patients (total n = 951,083). The investigators concluded that the metabolic syndrome is associated with a 2-fold increase in cardiovascular outcomes and a 1.5-fold increase in all-cause mortality rates. One of the ways to hit the metabolic syndrome is an utterly simplistic view on this concept as a predictive tool only. Of course, the presence of the metabolic syndrome possesses a definite predictive value, but first of all it is a widely accepted concept regarding a biological condition based on the complex and interrelated pathophysiological mechanisms starting from excess central adiposity and insulin resistance. Therefore, it is completely unfair to compare it with statistically constructed predictive tools, including stronger prognostic variables even unrelated to each other from the biological point of view. For example, in the criteria for metabolic syndrome (in contrast to Framingham score) age and cholesterol - presumably low density lipoprotein - cholesterol (LDL-C) - levels are not included, as well as a variety of strong predictors used in other risk-stratification scores: previous myocardial infarction, heart failure, smoking, family history, etc. However, the metabolic syndrome identifies additional important residual vascular risk mainly associated with insulin resistance and atherogenic dyslipidemia (low high density lipoprotein-cholesterol (HDL-C), high triglycerides, small, dense LDL-C). Therefore, the metabolic syndrome could be a useful additional contributor in estimation of global cardiovascular risk beyond age, high LDL-C or other standard risk factors. The components of the metabolic syndrome have partially overlapping mechanisms of pathogenic actions mediated through common metabolic pathways. Therefore their total combined effect could be less than the summed of the individual effects. The concept that the metabolic syndrome is a consequence of obesity and insulin resistance, provides a useful "life-style changes" approach for prevention and treatment: caloric restriction, weight-loss and increased physical activity. The next step could theoretically be pharmacological interventions such as metformin, acarbose, fibrates, weight-loss drugs (currently only orlistat is practically available) and perhaps glucagon-like peptide-1 agonists. A third step should probably be kept for bariatric surgery

The ubiquitous interleukin-6: a time for reappraisal

Interleukin-6 (IL-6) is a multifunctional cytokine regulating humoral and cellular responses and playing a central role in inflammation and tissue injury. Its effects are mediated through interaction with its receptor complex, IL-6Rβ (also known as gp130). It plays an important role in the pathogenesis of coronary artery disease and large quantities of IL-6 are found in human atherosclerotic plaques. IL-6 levels positively correlate with higher all-cause mortality, unstable angina, left ventricular dysfunction, propensity to diabetes and its complications, hypertension, obesity and several types of cancer. IL-6 levels augmentation demonstrates a remarkable parallel with another biomarkers reflecting harmful processes, like tumor necrosis factor alpha, interleukins 8 and 18, YKL-40, C reactive protein and resistin. Due to these facts, IL-6 was classified as a noxious interleukin. Nonetheless, there are several facts that challenge this usually accepted point of view. Since IL-6 has also anti-inflammatory activity, it seems reasonable to assume that favorable aspects exist. These aspects are two: 1. protection against bacterial infections, inactivating proinflammatory mediators, mitigating the course of septic shock and inducing the production of cortisol; and 2. influence on insulin sensitivity during exercise; this aspect is even more important. During exercise IL-6 is synthesized and released by muscles, with enhanced insulin action immediately at early recovery. Skeletal muscle may be considered as an endocrine organ; contracting muscles produce IL-6 and release it into the blood exerting its effects on other organs. The increase in circulating levels of IL-6 after exercise is consistent and proportional to exercise duration, intensity, muscle mass involved and endurance capacity. Thus, the fascinating possibility that the plenteous beneficial health effects of exercise could be ultimately mediated by IL-6 merits further elucidation. Interleukins were termed "good" or "bad", probably due to a tendency to see things in black and white, with no gray area in between. Calling IL-6 "a molecule with both beneficial and destructive potentials" would be a more equitable approach. In the literary creatures of Dr. Jekyll and Mr. Hyde, a good and an evil personality are found in the same individual. IL-6 playing the role of Dr. Jekyll is emerging; the time for IL-6 reappraisal is coming