scholarly journals In Silico and In Cell Analysis of Openable DNA Nanocages for miRNA Silencing

2019 ◽  
Vol 21 (1) ◽  
pp. 61
Author(s):  
Sofia Raniolo ◽  
Federico Iacovelli ◽  
Valeria Unida ◽  
Alessandro Desideri ◽  
Silvia Biocca
Keyword(s):  
Gel Electrophoresis ◽  
High Stability ◽  
Integrated Approach ◽  
Bond Number ◽  
Cell Analysis ◽  
Stable Conformation ◽  
Dna Hairpins ◽  
Open Conformation ◽  
Internal Volume ◽  
Dynamics Simulations

A computational and experimental integrated approach was applied in order to study the effect of engineering four DNA hairpins into an octahedral truncated DNA nanocage, to obtain a nanostructure able to recognize and bind specific oligonucleotide sequences. Modeling and classical molecular dynamics simulations show that the new H4-DNA nanocage maintains a stable conformation with the closed hairpins and, when bound to complementary oligonucleotides produces an opened conformation that is even more stable due to the larger hydrogen bond number between the hairpins and the oligonucleotides. The internal volume of the open conformation is much larger than the closed one, switching from 370 to 650 nm3, and the predicted larger conformational change is experimentally detectable by gel electrophoresis. H4-DNA nanocages display high stability in serum, can efficiently enter the cells where they are stable and maintain the ability to bind, and sequester an intracellular-specific oligonucleotide. Moreover, H4-DNA nanocages, modified in order to recognize the oncogenic miR21, are able to seize miRNA molecules inside cells in a selective manner.

Atom Condensed Fukui Function for Condensed Phases and Biological Systems and Its Application to Enzymatic Fixation of Carbon Dioxide

2019 ◽  
Author(s):  
Javier Oller ◽  
David A. Sáez ◽  
Esteban Vöhringer-Martinez
Keyword(s):  
Carbon Dioxide ◽  
Aqueous Solution ◽  
Molecular System ◽  
Chemical Reactivity ◽  
Nucleophilic Attack ◽  
Stable Conformation ◽  
Fukui Functions ◽  
Reactivity Descriptors ◽  
Dynamics Simulations ◽  
Fixation Of Carbon Dioxide

<div><div><div><p>Local reactivity descriptors such as atom condensed Fukui functions are promising computational tools to study chemical reactivity at specific sites within a molecule. Their applications have been mainly focused on isolated molecules in their most stable conformation without considering the effects of the surroundings. Here, we propose to combine QM/MM Born-Oppenheimer molecular dynamics simulations to obtain the microstates (configurations) of a molecular system using different representations of the molecular environment and calculate Boltzmann weighted atom condensed local reac- tivity descriptors based on conceptual DFT. Our approach takes the conformational fluctuations of the molecular system and the polarization of its electron density by the environment into account allowing us to analyze the effect of changes in the molecular environment on reactivity. In this contribution, we apply the method mentioned above to the catalytic fixation of carbon dioxide by crotonyl-CoA carboxylase/reductase and study if the enzyme alters the reactivity of its substrate compared to an aqueous solution. Our main result is that the protein en- vironment activates the substrate by the elimination of solute-solvent hydrogen bonds from aqueous solution in the two elementary steps of the reaction mechanism: the nucleophilic attack of a hydride anion from NADPH on the α, β unsaturated thioester and the electrophilic attack of carbon dioxide on the formed enolate species.</p></div></div></div>

Computer Simulations of Nonlinear Optical Chromophore Containing Polypeptides

1993 ◽  
Vol 330 ◽  
Author(s):  
Ruth Pachter ◽  
Steven B. Fairchild ◽  
James A. Lupo ◽  
Brian S. Sennett ◽  
Robert L. Crane ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Structure Prediction ◽  
Nonlinear Optical ◽  
Integrated Approach ◽  
Genetically Engineered ◽  
Spatial Proximity ◽  
Tertiary Structures ◽  
Eglin C ◽  
Nonlinear Optical Chromophores ◽  
Dynamics Simulations

ABSTRACTIn our continuing efforts towards the design of nonlinear (NLO) optical chromophore containing polypeptides we present an integrated computational approach, in which the design of biomolecular materials with defined secondary and tertiary structures is investigated by means of novel predictive tools, while the effects of the nonlinear optical chromophores are studied with molecular dynamics simulations. A neural network that was trained to predict the spatial proximity of Cα atoms that are less than a given threshold apart, is applied. The double-iterated Kalman filter (DIKF) technique is then employed with a constraints set that includes these pairwise atomic distances, and the distances and angles that define the structure as it is known from the protein's sequence. The results for test cases, particularly Crambin and genetically engineered Eglin-C, demonstrate that this integrated approach is useful for structure prediction at an intermediate resolution. Defined structural motifs of NLO chromophore containing polypeptides are investigated by using molecular dynamics techniques, particularly for the design of coil coiled amphiphatic biopolymers.

scholarly journals Molecular Simulations suggest Vitamins, Retinoids and Steroids as Ligands binding the Free Fatty Acid Pocket of SARS-CoV-2 Spike Protein

2020 ◽  
Author(s):  
Deborah Shoemark ◽  
Charlotte Colenso ◽  
Christine Toelzer ◽  
Kapil Gupta ◽  
Richard Sessions ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Binding Site ◽  
Spike Protein ◽  
Fatty Acid Binding ◽  
Open Conformation ◽  
Interaction Interface ◽  
Approved Drugs ◽  
Dynamics Simulations ◽  
Fatty Acid Binding Site

<p>Following our recent identification of a fatty acid binding site in the SARS-CoV-2 spike protein (Toelzer <i>et al., Science</i> eabd3255 (2020)), we investigate the binding of linoleate and other potential ligands at this site using molecular dynamics simulations. The results support the hypothesis that linoleate stabilises the locked form of the spike, in which its interaction interface for the ACE2 receptor is occluded. The simulations indicate weaker binding of linoleate to the partially open conformation. Simulations of dexamethasone bound at this site indicate that it binds similarly to linoleate, and thus may also stabilize a locked spike conformation. In contrast, simulations suggest that cholesterol bound at this site may destabilize the locked conformation, and in the open conformation, may preferentially bind at an alternative site in the hinge region between the receptor binding domain and the domain below, which could have functional relevance. We also use molecular docking to identify potential ligands that may bind at the fatty acid binding site, using the Bristol University Docking Engine (BUDE). BUDE docking successfully reproduces the linoleate complex and also supports binding of dexamethasone at the spike fatty acid site. Virtual screening of a library of approved drugs identifies vitamins D, K and A, as well as retinoid ligands with experimentally demonstrated activity against SARS-CoV-2 replication <i>in vitro</i>, as also potentially able to bind at this site. Our data suggest that the fatty acid binding site of the SARS-CoV-2 spike protein may bind a diverse array of candidate ligands. Targeting this site with small molecules, including dietary components such as vitamins, which may stabilise its locked conformation and represents a potential avenue for novel therapeutics or prophylaxis for COVID-19.</p>

scholarly journals Hydration of Simple Model Peptides in Aqueous Osmolyte Solutions

2021 ◽  
Vol 22 (17) ◽  
pp. 9350
Author(s):  
Aneta Panuszko ◽  
Maciej Pieloszczyk ◽  
Anna Kuffel ◽  
Karol Jacek ◽  
Karol A. Biernacki ◽  
...  
Keyword(s):  
High Stability ◽  
Water Molecules ◽  
Hydration Water ◽  
Computational Results ◽  
Protein Surface ◽  
Structure Of Water ◽  
Hydration Shells ◽  
Dynamics Simulations ◽  
Proteins And Peptides ◽  
Main Factor

The biology and chemistry of proteins and peptides are inextricably linked with water as the solvent. The reason for the high stability of some proteins or uncontrolled aggregation of others may be hidden in the properties of their hydration water. In this study, we investigated the effect of stabilizing osmolyte–TMAO (trimethylamine N-oxide) and destabilizing osmolyte–urea on hydration shells of two short peptides, NAGMA (N-acetyl-glycine-methylamide) and diglycine, by means of FTIR spectroscopy and molecular dynamics simulations. We isolated the spectroscopic share of water molecules that are simultaneously under the influence of peptide and osmolyte and determined the structural and energetic properties of these water molecules. Our experimental and computational results revealed that the changes in the structure of water around peptides, caused by the presence of stabilizing or destabilizing osmolyte, are significantly different for both NAGMA and diglycine. The main factor determining the influence of osmolytes on peptides is the structural-energetic similarity of their hydration spheres. We showed that the chosen peptides can serve as models for various fragments of the protein surface: NAGMA for the protein backbone and diglycine for the protein surface with polar side chains.

scholarly journals Integrating NMR and simulations reveals motions in the UUCG tetraloop

2020 ◽  
Vol 48 (11) ◽  
pp. 5839-5848 ◽  
Author(s):  
Sandro Bottaro ◽  
Parker J Nichols ◽  
Beat Vögeli ◽  
Michele Parrinello ◽  
Kresten Lindorff-Larsen
Keyword(s):  
Experimental Data ◽  
Three Dimensional ◽  
Machine Learning Techniques ◽  
Dimensional Structure ◽  
Stable Conformation ◽  
Stem Loop ◽  
Loop Region ◽  
Simple Model System ◽  
Nuclear Overhauser ◽  
Dynamics Simulations

Abstract We provide an atomic-level description of the structure and dynamics of the UUCG RNA stem–loop by combining molecular dynamics simulations with experimental data. The integration of simulations with exact nuclear Overhauser enhancements data allowed us to characterize two distinct states of this molecule. The most stable conformation corresponds to the consensus three-dimensional structure. The second state is characterized by the absence of the peculiar non-Watson–Crick interactions in the loop region. By using machine learning techniques we identify a set of experimental measurements that are most sensitive to the presence of non-native states. We find that although our MD ensemble, as well as the consensus UUCG tetraloop structures, are in good agreement with experiments, there are remaining discrepancies. Together, our results show that (i) the MD simulation overstabilize a non-native loop conformation, (ii) eNOE data support its presence with a population of ≈10% and (iii) the structural interpretation of experimental data for dynamic RNAs is highly complex, even for a simple model system such as the UUCG tetraloop.

Chloride-dependent conformational changes in the GlyT1 glycine transporter

2020 ◽  
Author(s):  
Yuan-Wei Zhang ◽  
Stacy Uchendu ◽  
Vanessa Leone ◽  
Richard T. Bradshaw ◽  
Ntumba Sangwa ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Ion Pair ◽  
Cysteine Residues ◽  
Glycine Transporter ◽  
Open Conformation ◽  
Transporter Family ◽  
Transport Cycle ◽  
Dynamics Simulations ◽  
Insight Into

AbstractThe human GlyT1 glycine transporter requires chloride for its function. However, the mechanism by which Cl- exerts its influence is unknown. To examine the role that Cl- plays in the transport cycle, we measured the effect of Cl- on both glycine binding and conformational changes. The ability of glycine to displace the high-affinity radioligand [3H]CHIBA-3007 required Na+ and was potentiated over 1000-fold by Cl-. We generated GlyT1b mutants containing reactive cysteine residues in either the extracellular or cytoplasmic permeation pathways and measured changes in the reactivity of those cysteine residues as indicators of conformational changes in response to ions and substrate. Na+ increased accessibility in the extracellular pathway and decreased it in the cytoplasmic pathway, consistent with stabilizing an outward-open conformation as observed in other members of this transporter family. In the presence of Na+, both glycine and Cl- independently shifted the conformation of GlyT1b toward an outward-closed conformation. Together, Na+, glycine and Cl- stabilized an inward-open conformation of GlyT1b. We then examined whether Cl- acts by interacting with a conserved glutamine to allow formation of an ion pair that stabilizes the closed state of the extracellular pathway. Molecular dynamics simulations of a GlyT1 homologue indicated that this ion pair is formed more frequently as that pathway closes. Mutation of the glutamine blocked the effect of Cl-, and substituting it with glutamate or lysine resulted in outward- or inward-facing transporter conformations, respectively. These results provide novel and unexpected insight into the role of Cl- in this family of transporters.

An Integrated Approach for an Articulated Bus Development. Durability and Dynamics Simulations

2004 ◽  
Author(s):  
Cristina Minioli Saracho ◽  
Celso Figueiredo Nogueira ◽  
Carlos Shigueru Miyoshi ◽  
Marcos Antonio Argentino
Keyword(s):  
Integrated Approach ◽  
Dynamics Simulations

scholarly journals Global and local mechanical properties control endonuclease reactivity of a DNA origami nanostructure

2020 ◽  
Vol 48 (9) ◽  
pp. 4672-4680 ◽  
Author(s):  
Antonio Suma ◽  
Alex Stopar ◽  
Allen W Nicholson ◽  
Matteo Castronovo ◽  
Vincenzo Carnevale
Keyword(s):  
Mechanical Properties ◽  
Dna Origami ◽  
Coarse Grained ◽  
Free Energy Barrier ◽  
Stable Conformation ◽  
Rational Engineering ◽  
Dynamics Simulations ◽  
Global Fluctuations ◽  
Global And Local ◽  
Good Agreement

Abstract We used coarse-grained molecular dynamics simulations to characterize the global and local mechanical properties of a DNA origami triangle nanostructure. The structure presents two metastable conformations separated by a free energy barrier that is lowered upon omission of four specific DNA staples (defect). In contrast, only one stable conformation is present upon removing eight staples. The metastability is explained in terms of the intrinsic conformations of the three trapezoidal substructures. We computationally modeled the local accessibility to endonucleases, to predict the reactivity of twenty sites, and found good agreement with the experimental data. We showed that global fluctuations affect local reactivity: the removal of the DNA staples increased the computed accessibility to a restriction enzyme, at sites as distant as 40 nm, due to an increase in global fluctuation. These results raise the intriguing possibility of the rational engineering of allosterically modulated DNA origami.

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