Stereochemical errors and their implications for molecular dynamics simulations

<p>Abstract</p> <p>Background</p> <p>Biological molecules are often asymmetric with respect to stereochemistry, and correct stereochemistry is essential to their function. Molecular dynamics simulations of biomolecules have increasingly become an integral part of biophysical research. However, stereochemical errors in biomolecular structures can have a dramatic impact on the results of simulations.</p> <p>Results</p> <p>Here we illustrate the effects that chirality and peptide bond configuration flips may have on the secondary structure of proteins throughout a simulation. We also analyze the most common sources of stereochemical errors in biomolecular structures and present software tools to identify, correct, and prevent stereochemical errors in molecular dynamics simulations of biomolecules.</p> <p>Conclusions</p> <p>Use of the tools presented here should become a standard step in the preparation of biomolecular simulations and in the generation of predicted structural models for proteins and nucleic acids.</p

Intramuscular long-acting paliperidone palmitate in acute patients with schizophrenia unsuccessfully treated with oral antipsychotics.

AbstractIn this prospective multicentre, open-label, 6-month study (Paliperidone Palmitate Flexible Dosing in Schizophrenia [PALMFlexS]), tolerability, safety and treatment response with paliperidone palmitate (PP) were explored in patients with acute symptoms of schizophrenia following switching from previously unsuccessful treatment with oral antipsychotics. This pragmatic study was conducted in a large, more representative sample of the general schizophrenia population compared to randomized controlled pivotal trials, to specifically mimic real-world clinical situations. After initiation on Day 1 and Day 8, patients received PP once monthly at flexible doses (50–150mgeq.) intramuscularly. The primary efficacy outcome was defined as the percentage of patients achieving ≥30% improvement in PANSS total score from baseline (BL) to last-observation-carried-forward (LOCF) endpoint (EP). Safety and tolerability assessments included Extrapyramidal Symptom Rating Scale (ESRS) total score and treatment-emergent adverse events (TEAEs). Overall, 212 patients received PP at least once after switching from oral antipsychotics, primarily due to lack of efficacy (45.8%). Significant improvements from BL in mean (SD) PANSS total score were observed from Day 8 onwards (BL to LOCF EP: −31.0 [29.0]; p<0.0001). At endpoint, two-thirds (66.7%) and 43.5% of patients achieved a ≥30% and ≥50% improvement in mean PANSS total score, respectively. PP was associated with significant improvements across secondary measures of symptom severity, subjective well-being, medication satisfaction, illness-related disorders of activity and participation, and patient functioning (p<0.0001; BL to LOCF EP). PP was generally well tolerated, with significant reductions in ESRS total score (p<0.0001) and mainly mild-to-moderate TEAEs. TEAEs reported in ≥5% of patients were injection-site pain (13.7%), insomnia (10.8%), psychotic disorder (10.4%), headache and anxiety (both 6.1%). The PALMFlexS study findings provide valuable pragmatic clinical data on PP treatment in patients with acute schizophrenia previously unsuccessfully treated with oral antipsychotics

A Prospective Flexible-Dose Study of Paliperidone Palmitate in Nonacute But Symptomatic Patients With Schizophrenia Previously Unsuccessfully Treated With Oral Antipsychotic Agents

AbstractPurposeThe goal of this study was to explore the tolerability, safety, and treatment response of flexible doses of once-monthly paliperidone palmitate (PP) in the subset of nonacute but symptomatic adult patients with schizophrenia previously unsuccessfully treated with oral antipsychotic agents in the PALMFlexS (Paliperidone Palmitate Flexible Dosing in Schizophrenia) study.MethodsThis was an interventional, single-arm, international, multicenter, unblinded, 6-month study performed in patients with schizophrenia. Patients were categorized according to reasons for switching. In patients switching because of lack of efficacy or for other reasons, primary efficacy outcomes were the proportion achieving treatment response (defined as ≥20% improvement in Positive and Negative Syndrome Scale [PANSS] total score from baseline to last-observation-carried-forward end point) and maintained efficacy (defined as noninferiority in the change in PANSS total score at end point versus baseline [Schuirmann's test]), respectively.FindingsA total of 593 patients (intention-to-treat population) were enrolled: 63.1% were male; their mean (SD) age was 38.4 (11.8) years; and 78.6% had paranoid schizophrenia. The main reasons for transition to PP were patient's wish (n = 259 [43.7%]), lack of efficacy (n = 144 [24.3%]), lack of compliance (n = 138 [23.3%]), and lack of tolerability (n = 52 [8.8%]) with the previous oral antipsychotic medication. The recommended PP initiation regimen (150 milligram equivalents [mg eq] day 1 and 100 mg eq day 8) was administered in 93.9% of patients. Mean PANSS total score decreased from 71.5 (14.6) at baseline to 59.7 (18.1) at end point (mean change, –11.7 [15.9]; 95% CI, –13.0 to –10.5; P < 0.0001). Sixty-four percent of patients showed an improvement of ≥20% in PANSS total score, and the percentage of patients rated mildly ill or less in Clinical Global Impression–Severity increased from 31.8% to 63.2%. Mean personal and social performance total score (SD) increased (ie, improved) significantly for all patients from baseline to end point (58.1 [13.4] to 66.1 [15.7]; P < 0.0001).ImplicationsThe PALMFlexS study is a pragmatic interventional study compared with randomized controlled trials, conducted in a large, more representative sample of patients with schizophrenia, and designed specifically to mimic real-world clinical situations. The findings support the results from randomized controlled studies. They also demonstrate that a clinically relevant treatment response is possible in patients who are considered to be clinically stable by their physician, supporting the use of flexibly dosed PP in such patients. Clinical trials.gov number: NCT01281527

Similar recovery time of microbial functions from fungicide stress across biogeographical regions

Abstract Determining whether the structural and functional stress responses of communities are similar across space and time is paramount for forecasting and extrapolating the consequences of anthropogenic pressures on ecosystems and their services. Stream ecosystems are under high anthropogenic pressure; however, studies have only examined the response of stream communities across large scales over multiple generations. We studied the responses of leaf-associated microbial communities in streams within three European biogeographical regions to chemical stress in a microcosm experiment with multiple cycles of fungicide pollution and resource colonisation. Fungal community composition and the ecosystem function leaf decomposition were measured as response variables. Microbial leaf decomposition showed similar recovery times under environmental levels of fungicide exposure across regions. Initially, the decomposition declined (between 19 and 53%) under fungicide stress and recovered to control levels during the third cycle of pollution and colonisation. Although community composition and its stress response varied between regions, this suggests similar functional community adaptation towards fungicide stress over time. Genetic, epigenetic and physiological adaptations, as well as species turnover, may have contributed to community adaptation but further studies are required to determine if and to which extent these mechanisms are operating. Overall, our findings provide the first evidence of a similar functional response of microbial leaf decomposition to chemical stress across space and time

Temperature Dependent Conformational Transitions and Hydrogen Bond Dynamics of the Elastin-Like Octapeptide GVG(VPGVG): a Molecular Dynamics Study

A joint experimental / theoretical investigation of the elastin-like octapeptide GVG(VPGVG) was carried out. In this paper a comprehensive molecular dynamics study of the temperature dependent folding and unfolding of the octapeptide is presented. The current study, as well as its experimental counterpart find that this peptide undergoes an "inverse temperature transition", ITT, leading to a folding at about 310-330 K. In addition, an unfolding transition is identified at unusually high temperatures approaching the boiling point of water. Due to the small size of the system two broad temperature regimes are found: the "ITT regime" (at about 280-320 K) and the "unfolding regime" at about T > 330 K, where the peptide has a maximum probability of being folded at approximately 330 K. A detailed molecular picture involving a thermodynamic order parameter, or reaction coordinate, for this process is presented along with a time-correlation function analysis of the hydrogen bond dynamics within the peptide as well as between the peptide and solvating water molecules. Correlation with experimental evidence and ramifications on the properties of elastin are discussed.Comment: 15 pages, 1 table, 8 figure

Domain Organization of Long Signal Peptides of Single-Pass Integral Membrane Proteins Reveals Multiple Functional Capacity

Targeting signals direct proteins to their extra - or intracellular destination such as the plasma membrane or cellular organelles. Here we investigated the structure and function of exceptionally long signal peptides encompassing at least 40 amino acid residues. We discovered a two-domain organization (“NtraC model”) in many long signals from vertebrate precursor proteins. Accordingly, long signal peptides may contain an N-terminal domain (N-domain) and a C-terminal domain (C-domain) with different signal or targeting capabilities, separable by a presumably turn-rich transition area (tra). Individual domain functions were probed by cellular targeting experiments with fusion proteins containing parts of the long signal peptide of human membrane protein shrew-1 and secreted alkaline phosphatase as a reporter protein. As predicted, the N-domain of the fusion protein alone was shown to act as a mitochondrial targeting signal, whereas the C-domain alone functions as an export signal. Selective disruption of the transition area in the signal peptide impairs the export efficiency of the reporter protein. Altogether, the results of cellular targeting studies provide a proof-of-principle for our NtraC model and highlight the particular functional importance of the predicted transition area, which critically affects the rate of protein export. In conclusion, the NtraC approach enables the systematic detection and prediction of cryptic targeting signals present in one coherent sequence, and provides a structurally motivated basis for decoding the functional complexity of long protein targeting signals

Biochemical aspects of iron-sulfur systems

Diese Arbeit behandelt grundlegende Aspekte der Magnetochemie von FeS-Proteinen (magnetostrukturelle Dynamik von Ferredoxin) und der Entstehung des Lebens in der "Eisen-Schwefel-Welt" (präbiotische Peptidsynthese). Durch ab initio Molekulardynamik und eine neue Spinprojektions-Methode wurde ein dynamisches Wechselspiel zwischen dem magnetischen Austausch und spezifischen Vibrationsmoden des [2Fe2S] Clusters entdeckt, wobei Wasserstoffbrücken zwischen dem Cluster und dem Protein dieses modulieren. Damit wird das Verständnis der magnetostrukturellen Korrelationen über die Goodenough-Kanamori-Regeln hinaus erweitert. Ein Peptidsynthese-Zyklus wurde mit ab initio Metadynamik in wässiger Losung bei Normalbedingungen, in heissem Wasser unter Druck und an der Grenzfläche zwischen heissem Wasser und Pyrit untersucht. Der Cyklus ist unter allen Bedingungen produktiv, jedoch wird die Peptidsynthese durch extreme Bedingungen und die Katalyse durch die Pyritoberfläche gefördert.This thesis aims to shed light on basic aspects of the magnetochemistry of iron-sulfur proteins and of the origin of life in the "Iron-Sulfur-World", particularly magnetostructural dynamics of ferredoxin and prebiotic peptide synthesis. By a novel spin projection method and ab initio molecular dynamics an intimate interplay of the magnetic exchange and specific vibrational modes of the [2Fe2S] cluster as well as hydrogen bonds of the cluster to the protein was discovered, thus going beyond the Goodenough-Kanamori rules for magnetostructural correlations. Using ab initio metadynamics a synthesis cycle for peptide formation in hot-pressurized water and at a pyrite-hot-water interface is provided and compared to ambient aqueous conditions. The formation of Leuchs anhydride is found to follow a route via isocyanate. Altough all studied conditions yield a productive cycle, extreme conditions and the pyrite surface as catalyst favor peptide synthesis in comparison to ambient conditions

Mechanisms of SecM-Mediated Stalling in the Ribosome

ABSTRACT Nascent-peptide modulation of translation is a common regulatory mechanism of gene expression. In this mechanism, while the nascent peptide is still in the exit tunnel of the ribosome, it induces translational pausing, thereby controlling the expression of downstream genes. One example is SecM, which inhibits peptide-bond formation in the ribosome’s peptidyl transferase center (PTC) during its own translation, upregulating the expression of the protein translocase SecA. Although biochemical experiments and cryo-electron microscopy data have led to the identification of some residues involved in SecM recognition, the full pathway of interacting residues that connect SecM to the PTC through the ribosome has not yet been conclusively established. Here, using the cryo-electron microscopy data, we derived the first (to our knowledge) atomic model of the SecM-stalled ribosome via molecular-dynamics flexible fitting, complete with P- and A-site tRNAs. Subsequently, we carried out simulations of native and mutated SecM-stalled ribosomes to investigate possible interaction pathways between a critical SecM residue, R163, and the PTC. In particular, the simulations reveal the role of SecM in altering the position of the tRNAs in the ribosome, and thus demonstrate how the presence of SecM in the exit tunnel induces stalling. Finally, steered molecular-dynamics simulations in which SecM was pulled toward the tunnel exit suggest how SecA interacting with SecM from outside the ribosome relieves stalling

Closed-Form Coexistence Equation for Phase Separation of Polymeric Mixtures in Dissipative Particle Dynamics

To date, no extensive study of the phase diagram for binary fluid mixtures in dissipative particle dynamics (DPD) has been published. This is especially pertinent for newer parameterization schemes where the self-self interaction, or the effective volume, of different particle types is varied. This work presents an exhaustive study of the parameter space concerning DPD particles with soft interaction potentials. Moreover, we propose a closed-form coexistence equation or binodal curve that is inspired by the Flory-Huggins model. This equation describes the phase diagram of all binary mixtures made up out of monomers, homopolymers, and the mixtures thereof when self-self interactions are varied. The mean absolute percentage error (MAPE) of the equation on simulated data, including validation simulations, is 1.02%. The equation can a priori predict the phase separation of mixtures using only DPD interaction parameters. The proposed coexistence equation can therefore be used to directly validate interaction parameters resulting from novel parameterization schemes, including coarse graining and equations of state, without the need for additional simulations. Finally, it is shown that the choice of bond potential markedly influences phase behavior