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

Since its early days in the 19th century, medicinal chemistry has concentrated its efforts on the treatment of diseases, using tools from areas such as chemistry, pharmacology, and molecular biology. The understanding of biological mechanisms and signaling pathways is crucial information for the development of potential agents for the treatment of diseases mainly because they are such complex processes. Given the limitations that the experimental approach presents, computational chemistry is a valuable alternative for the study of these systems and their behavior. Thus, classical molecular dynamics, based on Newton's laws, is considered a technique of great accuracy, when appropriated force fields are used, and provides satisfactory contributions to the scientific community. However, as many configurations are generated in a large MD simulation, methods such as Statistical Inefficiency and Optimal Wavelet Signal Compression Algorithm are great tools that can reduce the number of subsequent QM calculations. Accordingly, this review aims to briefly discuss the importance and relevance of medicinal chemistry allied to computational chemistry as well as to present a case study where, through a molecular dynamics simulation of AMPK protein (50 ns) and explicit solvent (TIP3P model), a minimum number of snapshots necessary to describe the oscillation profile of the protein behavior was proposed. For this purpose, the RMSD calculation, together with the sophisticated OWSCA method was used to propose the minimum number of snapshots.

• Klíčová slova
• Medicinal chemistry, OWSCA, computational chemistry., conformational choice, molecular dynamics, snapshots,
• MeSH
• algoritmy MeSH
• chemie farmaceutická MeSH
• kvantová teorie MeSH
• lidé MeSH
• proteinkinasy aktivované AMP metabolismus   chemie   MeSH
• simulace molekulární dynamiky * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH
• Názvy látek
• proteinkinasy aktivované AMP MeSH

With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are intimately linked to its structure and dynamics. Computer simulations, and in particular atomistic molecular dynamics (MD), allow structural dynamics of biomolecular systems to be investigated with unprecedented temporal and spatial resolution. We here provide a comprehensive overview of the fast-developing field of MD simulations of RNA molecules. We begin with an in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods. We also survey the closely related field of coarse-grained modeling of RNA systems. After dealing with the methodological aspects, we provide an exhaustive overview of the available RNA simulation literature, ranging from studies of the smallest RNA oligonucleotides to investigations of the entire ribosome. Our review encompasses tetranucleotides, tetraloops, a number of small RNA motifs, A-helix RNA, kissing-loop complexes, the TAR RNA element, the decoding center and other important regions of the ribosome, as well as assorted others systems. Extended sections are devoted to RNA-ion interactions, ribozymes, riboswitches, and protein/RNA complexes. Our overview is written for as broad of an audience as possible, aiming to provide a much-needed interdisciplinary bridge between computation and experiment, together with a perspective on the future of the field.

• MeSH
• DNA chemie   MeSH
• katalýza MeSH
• konformace nukleové kyseliny * MeSH
• počítačová simulace MeSH
• RNA chemie   MeSH
• simulace molekulární dynamiky * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH
• Research Support, N.I.H., Extramural MeSH
• Názvy látek
• DNA MeSH
• RNA MeSH

In this work, we evaluated the valorisation of agricultural waste materials by transforming coconut husks and shells, corncobs and rice straw into biochar for water treatment in aquaculture. We compared the biochars' suitability for removal of organic micropollutants (acetaminophen, oxytetracycline, tetracycline, enrofloxacin, atrazine, diuron and diclofenac) from surface water needed for aquaculture. The biochars were prepared by three methods ranging from inexpensive drum kilns (200 °C) to pyrolysis with biogasfication (350-750 °C). Overall, antibiotics tetracycline and enrofloxacin were the most strongly sorbed micropollutants, and coconut husk biochar prepared at 750 °C was the best sorbent material. Molecular Dynamics simulations indicated that the major sorption mechanism is via π-π stacking interactions and there is a possibility of multilayer sorption for some of the micropollutants. We observed, a strong impact of ionic strength (salinity), which is an important consideration in coastal aquaculture applications. High salinity decreased the sorption for antibiotics oxytetracycline, tetracycline and enrofloxacin but increased diclofenac, atrazine and diuron sorption. We considered coconut husk biochar produced in drum kilns the most practical option for biochar applications in small-scale coastal aquacultures in South Asia. Pilot trials of canal water filtration at an aquaculture farm revealed that micropollutant sorption by coconut husk biochar under real-world conditions might be 10-500 times less than observed in the laboratory studies. Even so, biochar amendment of sand enhanced the micropollutant retention, which may facilitate subsequent biodegradation and improve the quality of brackish surface water used for food production in coastal aquaculture.

• Klíčová slova
• Agricultural waste, Aquaculture, Biochar, Micropollutants, Molecular dynamics simulations, Sorption,
• MeSH
• adsorpce MeSH
• dřevěné a živočišné uhlí MeSH
• simulace molekulární dynamiky * MeSH
• voda * MeSH
• vodní hospodářství MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• biochar MeSH Prohlížeč
• dřevěné a živočišné uhlí MeSH
• voda * 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

We provide a critical assessment of explicit-solvent atomistic molecular dynamics (MD) simulations of RNA and protein/RNA complexes, written primarily for non-specialists with an emphasis to explain the limitations of MD. MD simulations can be likened to hypothetical single-molecule experiments starting from single atomistic conformations and investigating genuine thermal sampling of the biomolecules. The main advantage of MD is the unlimited temporal and spatial resolution of positions of all atoms in the simulated systems. Fundamental limitations are the short physical time-scale of simulations, which can be partially alleviated by enhanced-sampling techniques, and the highly approximate atomistic force fields describing the simulated molecules. The applicability and present limitations of MD are demonstrated on studies of tetranucleotides, tetraloops, ribozymes, riboswitches and protein/RNA complexes. Wisely applied simulations respecting the approximations of the model can successfully complement structural and biochemical experiments. WIREs RNA 2017, 8:e1405. doi: 10.1002/wrna.1405 For further resources related to this article, please visit the WIREs website.

• MeSH
• konformace nukleové kyseliny MeSH
• lidé MeSH
• proteiny vázající RNA chemie   metabolismus   MeSH
• RNA chemie   metabolismus   MeSH
• simulace molekulární dynamiky * MeSH
• výpočetní biologie metody   MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH
• Názvy látek
• proteiny vázající RNA MeSH
• RNA MeSH

G-quadruplexes (G4s) are non-canonical nucleic acid structures that fold through complex processes. Characterization of the G4 folding landscape may help to elucidate biological roles of G4s but is challenging both experimentally and computationally. Here, we achieved complete folding of a three-quartet parallel DNA G4 with (GGGA)3GGG sequence using all-atom explicit-solvent enhanced-sampling molecular dynamics (MD) simulations. The simulations suggested early formation of guanine stacks in the G-tracts, which behave as semi-rigid blocks in the folding process. The folding continues via the formation of a collapsed compact coil-like ensemble. Structuring of the G4 from the coil then proceeds via various cross-like, hairpin, slip-stranded and two-quartet ensembles and can bypass the G-triplex structure. Folding of the parallel G4 does not appear to involve any salient intermediates and is a multi-pathway process. We also carried out an extended set of simulations of parallel G-hairpins. While parallel G-hairpins are extremely unstable when isolated, they are more stable inside the coil structure. On the methodology side, we show that the AMBER DNA force field predicts the folded G4 to be less stable than the unfolded ensemble, uncovering substantial force-field issues. Overall, we provide unique atomistic insights into the folding landscape of parallel-stranded G4 but also reveal limitations of current state-of-the-art MD techniques.

• Klíčová slova
• Folding, G-Quadruplex, Molecular dynamics,
• MeSH
• DNA chemie   MeSH
• G-kvadruplexy * MeSH
• konformace nukleové kyseliny MeSH
• nukleové kyseliny * MeSH
• simulace molekulární dynamiky MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• DNA MeSH
• nukleové kyseliny * 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

Hyaluronan is a natural carbohydrate polymer with a negative charge that fosters gel-like conditions crucial for its cellular functions and industrial applications. As a recognized ligand for proteins, understanding their mutual interactions provides solid ground to tune hyaluronan's gel properties using biocompatible peptides. This work employs NMR and molecular dynamics simulations to identify molecular motifs relevant to hyaluronan-peptide interactions using arginine, lysine, and glycine oligopeptides. Arginine-rich peptides exhibit the strongest binding to hyaluronan according to chemical shift perturbation measurements, followed distantly by the similarly charged lysine. This difference highlights the significance of electrostatics and the peculiarities of the guanidinium side chain in arginine, capable of non-polar interactions that further stabilize the binding. Additional nuclear Overhauser effect measurements do not show stable interaction partners, precluding strong and well-defined complexes. Finally, molecular simulations support our findings and show an extended but significant interaction region, especially for arginine, responsible for the observed enhanced binding, which can also promote cross-linking of hyaluronan polymers. Our findings pave the way for optimizing biocompatible peptides to alter hyaluronan gels' properties efficiently and also explain why hyaluronan-protein interaction typically involves positively charged arginine-rich regions also capable of forming hydrogen bonds and non-polar interactions.

• Klíčová slova
• Arginine, Hyaluronan, Molecular dynamics, NMR, Sugar–peptide interactions,
• MeSH
• arginin * chemie   MeSH
• kyselina hyaluronová * chemie   MeSH
• lysin chemie   MeSH
• peptidy chemie   MeSH
• simulace molekulární dynamiky MeSH
• statická elektřina MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• arginin * MeSH
• kyselina hyaluronová * MeSH
• lysin MeSH
• peptidy 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