Biomolecular simulations are routinely used in biochemistry and molecular biology research; however, they often fail to match expectations of their impact on pharmaceutical and biotech industry. This is caused by the fact that a vast amount of computer time is required to simulate short episodes from the life of biomolecules. Several approaches have been developed to overcome this obstacle, including application of massively parallel and special purpose computers or non-conventional hardware. Methodological approaches are represented by coarse-grained models and enhanced sampling techniques. These techniques can show how the studied system behaves in long time-scales on the basis of relatively short simulations. This review presents an overview of new simulation approaches, the theory behind enhanced sampling methods and success stories of their applications with a direct impact on biotechnology or drug design.

• Klíčová slova
• Alchemistic simulations, Drug design, Free energy surface, Metadynamics, Molecular dynamics simulation, Parallel tempering,
• MeSH
• metody pro přípravu analytických vzorků metody   MeSH
• simulace molekulární dynamiky * MeSH
• termodynamika MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH

Knowledge of the structure and conformational flexibility of carbohydrates in an aqueous solvent is important to improving our understanding of how carbohydrates function in biological systems. In this study, we extend a variant of the Hamiltonian replica-exchange molecular dynamics (MD) simulation to improve the conformational sampling of saccharides in an explicit solvent. During the simulations, a biasing potential along the glycosidic-dihedral linkage between the saccharide monomer units in an oligomer is applied at various levels along the replica runs to enable effective transitions between various conformations. One reference replica runs under the control of the original force field. The method was tested on disaccharide structures and further validated on biologically relevant blood group B, Lewis X and Lewis A trisaccharides. The biasing potential-based replica-exchange molecular dynamics (BP-REMD) method provided a significantly improved sampling of relevant conformational states compared with standard continuous MD simulations, with modest computational costs. Thus, the proposed BP-REMD approach adds a new dimension to existing carbohydrate conformational sampling approaches by enhancing conformational sampling in the presence of solvent molecules explicitly at relatively low computational cost.

• Klíčová slova
• adaptive biasing force simulations, biasing potential replica-exchange simulation, conformational sampling, molecular dynamics simulation, saccharides,
• MeSH
• antigeny krevních skupin chemie   genetika   MeSH
• disacharidy chemie   genetika   MeSH
• konformace sacharidů MeSH
• lidé MeSH
• sekvenční analýza * MeSH
• simulace molekulární dynamiky * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• antigeny krevních skupin MeSH
• disacharidy MeSH

OBJECTIVE: The impact of enhanced recovery after surgery (ERAS) protocol on postoperative outcomes after urogynecological surgery is yet to be a matter of investigation. This study sought to evaluate this issue by comparing the patients who had conventional or ERAS--guided perioperative care for several clinical end-points including ambulation, length of hospital stay (LOS), readmissions, and postoperative complications. MATERIALS AND METHODS: A total of 121 patients undergoing pelvic organ prolapse surgery were allocated to two study arms, ERAS protocol (Group E) or conventional care (Group C). Variables reflecting the restoration of appetite and bowel movements, bleeding events, other complications, LOS and readmissions were compared between the groups. RESULTS: The patients in Group C significantly received a more intensive intravenous fluid treatment compared to Group E (2,760 ± 656 vs. 1,045 ± 218 mL, P < 0.001). Time required for first flatus, first defecation, eating solid food, and ambulation (P < 0.001) were also longer in the former group of patients. Moreover, LOS was significantly reduced when the ERAS protocol was applied (2.5 ± 1.1 vs. 2.0 ± 0.6 days, P < 0.001). On the other hand, the two groups were similar with respect to the frequency of the postoperative complications, including surgical site infections, cardiovascular complications, non-specific abdominal pain, sub-ileus, blood loss and readmission rate. CONCLUSION: In our sample population, ERAS protocol led to early initiation of oral intake, early recovery of bowel function, early mobilization, and early discharge of patients without compromise in safety concerns after urogynecological surgery.

• Klíčová slova
• Enhanced Recovery After Surgery, Gynecologic surgery, pelvic organ prolapse, postoperative care, postoperative complications,
• MeSH
• délka pobytu MeSH
• lidé MeSH
• perioperační péče MeSH
• pooperační komplikace etiologie   MeSH
• pooperační období MeSH
• prolaps pánevních orgánů * komplikace   chirurgie   MeSH
• retrospektivní studie MeSH
• urychlená pooperační rehabilitace * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH

The temporomandibular joint (TMJ) is typically involved in 45-87% of children with Juvenile Idiopathic Arthritis (JIA). Accurate diagnosis of JIA is difficult as various clinical tests, including MRI, disagree. The purpose of this study is to optimize the methodological aspects of Dynamic Contrast Enhanced (DCE) MRI of the TMJ in children. In this cross-sectional study, including data from 73 JIA affected children, aged 6-15 years, effects of motion correction, sampling rate and parametric modelling on DCE-MRI data is investigated. Consensus among three radiologists determined the regions of interest. Quantitative perfusion parameters were estimated using four perfusion models; the Adiabatic Approximation to Tissue Homogeneity (AATH), Distributed Capillary Adiabatic Tissue Homogeneity (DCATH), Gamma Capillary Transit Time (GCTT) and Two Compartment Exchange (2CXM) models. Effects of motion correction were evaluated by a sum of least squares between corrected raw data and the GCTT model. The effect of systematically down sampling the raw data was tested. The sum of least squares was computed across all pharmacokinetic models. Relative difference perfusion parameters between the left and right TMJ were used for an unsupervised k-means based stratification of the data based on a principal component analysis, as well as for a supervised random forest classification. Diagnostic sensitivity and specificity were computed relative to structural image scorings. Paired sample t-tests, as well as ANOVA tests, were used (significant threshold: p < 0.05) with Tukeys post hoc test. High-level elastic motion correction provides the best least square fit to the GCTT model (percental improvement: 72-84%). A 4 s sampling rate captures more of the potentially disease relevant signal variations. The various parametric models all leave comparable residues (relative standard deviation: 3.4%). In further evaluation of DCE-MRI as a potential diagnostic tool for JIA a high-level elastic motion correction scheme should be adopted, with a sampling rate of at least 4 s. Results suggest that DCE-MRI data can be a valuable part in JIA diagnostics in the TMJ.

• Klíčová slova
• DCE MRI, JIA, Motion correction, Sampling rate, TMJ,
• MeSH
• artefakty MeSH
• dítě MeSH
• juvenilní artritida diagnostické zobrazování   MeSH
• lidé MeSH
• magnetická rezonanční tomografie * MeSH
• mladiství MeSH
• počítačové zpracování obrazu * MeSH
• pohyb * MeSH
• předškolní dítě MeSH
• průřezové studie MeSH
• senzitivita a specificita MeSH
• statistické modely * MeSH
• temporomandibulární kloub diagnostické zobrazování   MeSH
• Check Tag
• dítě MeSH
• lidé MeSH
• mladiství MeSH
• mužské pohlaví MeSH
• předškolní dítě MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Atomistic molecular dynamics simulations represent an established technique for investigation of RNA structural dynamics. Despite continuous development, contemporary RNA simulations still suffer from suboptimal accuracy of empirical potentials (force fields, ffs) and sampling limitations. Development of efficient enhanced sampling techniques is important for two reasons. First, they allow us to overcome the sampling limitations, and second, they can be used to quantify ff imbalances provided they reach a sufficient convergence. Here, we study two RNA tetraloops (TLs), namely the GAGA and UUCG motifs. We perform extensive folding simulations and calculate folding free energies (ΔGfold°) with the aim to compare different enhanced sampling techniques and to test several modifications of the nonbonded terms extending the AMBER OL3 RNA ff. We demonstrate that replica-exchange solute tempering (REST2) simulations with 12-16 replicas do not show any sign of convergence even when extended to a timescale of 120 μs per replica. However, the combination of REST2 with well-tempered metadynamics (ST-MetaD) achieves good convergence on a timescale of 5-10 μs per replica, improving the sampling efficiency by at least 2 orders of magnitude. Effects of ff modifications on ΔGfold° energies were initially explored by the reweighting approach and then validated by new simulations. We tested several manually prepared variants of the gHBfix potential which improve stability of the native state of both TLs by ∼2 kcal/mol. This is sufficient to conveniently stabilize the folded GAGA TL while the UUCG TL still remains under-stabilized. Appropriate adjustment of van der Waals parameters for C-H···O5' base-phosphate interaction may further stabilize the native states of both TLs by ∼0.6 kcal/mol.

• MeSH
• entropie MeSH
• RNA * chemie   MeSH
• simulace molekulární dynamiky * MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• RNA * MeSH

In this article, we present an enhanced sampling method based on a hybrid Hamiltonian which combines experimental distance restraints with a bias dependent from multiple path-dependent variables. This simulation method determines the bias-coordinates on the fly and does not require a priori knowledge about reaction coordinates. The hybrid Hamiltonian accelerates the sampling of proteins, and, combined with experimental distance information, the technique considers the restraints adaptively and in dependency of the system's intrinsic dynamics. We validate the methodology on the dipole relaxation of two water models and the conformational landscape of dialanine. Using experimental NMR-restraint data, we explore the folding landscape of the TrpCage mini-protein and in a second example apply distance restraints from chemical crosslinking/mass spectrometry experiments for the sampling of the conformation space of the Killer Cell Lectin-like Receptor Subfamily B Member 1A (NKR-P1A). The new methodology has the potential to adaptively introduce experimental restraints without affecting the conformational space of the system along an ergodic trajectory. Since only a limited number of input- and no-order parameters are required for the setup of the simulation, the method is broadly applicable and has the potential to be combined with coarse-graining methods.

• Klíčová slova
• enhanced molecular dynamics simulations, protein folding,
• MeSH
• časové faktory MeSH
• magnetická rezonanční spektroskopie MeSH
• peptidy chemie   MeSH
• simulace molekulární dynamiky * MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• peptidy MeSH

The RNA recognition motif (RRM) is the most common RNA binding domain across eukaryotic proteins. It is therefore of great value to engineer its specificity to target RNAs of arbitrary sequence. This was recently achieved for the RRM in Rbfox protein, where four mutations R118D, E147R, N151S, and E152T were designed to target the precursor to the oncogenic miRNA 21. Here, we used a variety of molecular dynamics-based approaches to predict specific interactions at the binding interface. Overall, we have run approximately 50 microseconds of enhanced sampling and plain molecular dynamics simulations on the engineered complex as well as on the wild-type Rbfox·pre-miRNA 20b from which the mutated systems were designed. Comparison with the available NMR data on the wild type molecules (protein, RNA, and their complex) served to establish the accuracy of the calculations. Free energy calculations suggest that further improvements in affinity and selectivity are achieved by the S151T replacement.

• MeSH
• konformace nukleové kyseliny MeSH
• lidé MeSH
• mikro RNA chemie   genetika   metabolismus   MeSH
• molekulární modely MeSH
• motiv rozpoznávající RNA * genetika   MeSH
• nukleární magnetická rezonance biomolekulární MeSH
• proteinové inženýrství MeSH
• proteiny vázající RNA chemie   genetika   metabolismus   MeSH
• RNA chemie   metabolismus   MeSH
• sekvence aminokyselin MeSH
• simulace molekulární dynamiky MeSH
• stabilita RNA MeSH
• vazba proteinů MeSH
• vazebná místa genetika   MeSH
• výpočetní biologie MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• mikro RNA MeSH
• MIRN20b microRNA, human MeSH Prohlížeč
• MIRN21 microRNA, human MeSH Prohlížeč
• proteiny vázající RNA MeSH
• RNA MeSH

The freely dissolved concentration of persistent organic pollutants (POPs) is one of the most important parameters for risk assessment in aquatic environments, due to its proportionality to the chemical activity. Chemical activity difference represents the driving force for a spontaneous contaminant transport, such as water-aquatic biota or water-sediment. Freely dissolved concentrations in sediment pore water can be estimated from the concentrations in a partition-based passive sampler equilibrated in suspensions of contaminated sediment. Equilibration in the sediment/passive sampler system is slow, since concentrations of most POPs in the water phase, which is the main route for mass transfer, are very low. Adding methanol to sediment in suspension increases the POPs' solubility and, consequently, the permeability in the water phase. The resulting higher aqueous concentrations enhance POPs mass transfer up to three times for investigated POPs (polycyclic aromatic hydrocarbons, polychlorinated biphenyls, organochlorine pesticides) and shorten equilibrium attainment to less than 6 weeks. The addition of methanol to the aqueous phase up to a molar fraction of 0.2 changed the POPs equilibrium distribution ratio between sediment and passive sampler by less than a factor of two. As a result, the pore water concentrations of POPs, calculated from their amounts accumulated in a passive sampler, are affected by methanol addition not more than by the same factor.

• Klíčová slova
• Mass transfer, Partitioning, Passive sampling, Persistent organic pollutants, Sediment,
• MeSH
• chemické látky znečišťující vodu analýza   MeSH
• chlorované uhlovodíky analýza   MeSH
• geologické sedimenty analýza   MeSH
• methanol chemie   MeSH
• monitorování životního prostředí metody   MeSH
• pesticidy analýza   MeSH
• polychlorované bifenyly analýza   MeSH
• polycyklické aromatické uhlovodíky analýza   MeSH
• rozpustnost MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• chemické látky znečišťující vodu MeSH
• chlorované uhlovodíky MeSH
• methanol MeSH
• pesticidy MeSH
• polychlorované bifenyly MeSH
• polycyklické aromatické uhlovodíky MeSH

A "dynamic" passive sampling (DPS) device, consisting of an electrically driven large volume water pumping device coupled to a passive sampler exposure cell, was designed to enhance the sampling rate of trace organic compounds. The purpose of enhancing the sampling rate was to achieve sufficient method sensitivity, when the period available for sampling is limited to a few days. Because the uptake principle in the DPS remains the same as for conventionally-deployed passive samplers, free dissolved concentrations can be derived from the compound uptake using available passive sampler calibration parameters. This was confirmed by good agreement between aqueous concentrations of polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs) and hexachlorobenzene (HCB) derived from DPS and conventional caged passive sampler. The DPS device enhanced sampling rates of compounds that are accumulated in samplers under water boundary layer control (WBL) more than five times compared with the conventionally deployed samplers. The DPS device was deployed from a ship cruising downstream the Danube River to provide temporally and spatially integrated concentrations. A DPS-deployed sampler with surface area of 400cm2 can reach sampling rates up to 83Ld-1. The comparison of three passive samplers made of different sorbents and co-deployed in the DPS device, namely silicone rubber (SR), low density polyethylene (LDPE) and SDB-RPS Empore™ disks showed a good correlation of surface specific uptake for compounds that were sampled integratively during the entire exposure period. This provided a good basis for a cross-calibration between the samplers. The good correlation of free dissolved PAHs, PCBs and HCB concentration estimates obtained using SR and LDPE confirmed that both samplers are suitable for the identification of concentration gradients and trends in the water column. We showed that the differences in calculated aqueous concentrations between sampler types are mainly associated with different applied uptake models.

• Klíčová slova
• Joint Danube survey, Mass transfer, Passive sampling, Trace organic compounds, Water quality,
• MeSH
• chemické látky znečišťující vodu analýza   MeSH
• monitorování životního prostředí přístrojové vybavení   MeSH
• polychlorované bifenyly analýza   MeSH
• polycyklické aromatické uhlovodíky analýza   MeSH
• řeky chemie   MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• chemické látky znečišťující vodu MeSH
• polychlorované bifenyly MeSH
• polycyklické aromatické uhlovodíky MeSH

In this article, we present a method for the enhanced molecular dynamics simulation of protein and DNA systems called potential of mean force (PMF)-enriched sampling. The method uses partitions derived from the potentials of mean force, which we determined from DNA and protein structures in the Protein Data Bank (PDB). We define a partition function from a set of PDB-derived PMFs, which efficiently compensates for the error introduced by the assumption of a homogeneous partition function from the PDB datasets. The bias based on the PDB-derived partitions is added in the form of a hybrid Hamiltonian using a renormalization method, which adds the PMF-enriched gradient to the system depending on a linear weighting factor and the underlying force field. We validated the method using simulations of dialanine, the folding of TrpCage, and the conformational sampling of the Dickerson⁻Drew DNA dodecamer. Our results show the potential for the PMF-enriched simulation technique to enrich the conformational space of biomolecules along their order parameters, while we also observe a considerable speed increase in the sampling by factors ranging from 13.1 to 82. The novel method can effectively be combined with enhanced sampling or coarse-graining methods to enrich conformational sampling with a partition derived from the PDB.

• Klíčová slova
• DNA simulation, enhanced molecular dynamics simulations, protein folding,
• MeSH
• databáze proteinů * MeSH
• DNA * chemie   genetika   MeSH
• počítačová simulace * MeSH
• sbalování proteinů * MeSH
• simulace molekulární dynamiky * MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• DNA * MeSH