scholarly journals In-Depth Molecular Dynamics Study of All Possible Chondroitin Sulfate Disaccharides Reveals Key Insight into Structural Heterogeneity and Dynamism

Biomolecules ◽  
2022 ◽  
Vol 12 (1) ◽  
pp. 77
Author(s):  
Balaji Nagarajan ◽  
Nehru Viji Sankaranarayanan ◽  
Umesh R. Desai
Keyword(s):  
Molecular Dynamics ◽  
Chondroitin Sulfate ◽  
Building Blocks ◽  
Structural Heterogeneity ◽  
Conformational Space ◽  
Protein Recognition ◽  
Production Run ◽  
Counter Ions ◽  
The Stability ◽  
High Level

GAGs exhibit a high level of conformational and configurational diversity, which remains untapped in terms of the recognition and modulation of proteins. Although GAGs are suggested to bind to more than 800 biologically important proteins, very few therapeutics have been designed or discovered so far. A key challenge is the inability to identify, understand and predict distinct topologies accessed by GAGs, which may help design novel protein-binding GAG sequences. Recent studies on chondroitin sulfate (CS), a key member of the GAG family, pinpointing its role in multiple biological functions led us to study the conformational dynamism of CS building blocks using molecular dynamics (MD). In the present study, we used the all-atom GLYCAM06 force field for the first time to explore the conformational space of all possible CS building blocks. Each of the 16 disaccharides was solvated in a TIP3P water box with an appropriate number of counter ions followed by equilibration and a production run. We analyzed the MD trajectories for torsional space, inter- and intra-molecular H-bonding, bridging water, conformational spread and energy landscapes. An in-house phi and psi probability density analysis showed that 1→3-linked sequences were more flexible than 1→4-linked sequences. More specifically, phi and psi regions for 1→4-linked sequences were held within a narrower range because of intra-molecular H-bonding between the GalNAc O5 atom and GlcA O3 atom, irrespective of sulfation pattern. In contrast, no such intra-molecular interaction arose for 1→3-linked sequences. Further, the stability of 1→4-linked sequences also arose from inter-molecular interactions involving bridged water molecules. The energy landscape for both classes of CS disaccharides demonstrated increased ruggedness as the level of sulfation increased. The results show that CS building blocks present distinct conformational dynamism that offers the high possibility of unique electrostatic surfaces for protein recognition. The fundamental results presented here will support the development of algorithms that help to design longer CS chains for protein recognition.

scholarly journals Abstract P-19: 15-Microsecond Molecular Dynamics Simulations of Nucleosome Show Structural Heterogeneity and Plasticity

2021 ◽  
Vol 11 (Suppl_1) ◽  
pp. S19-S20
Author(s):  
Grigoriy Armeev ◽  
Anastasiia Kniazeva ◽  
Galina Komarova ◽  
Mikhail Kirpichnikov ◽  
Alexey Shaytan
Keyword(s):  
Molecular Dynamics ◽  
Crystal Structures ◽  
Dna Sequences ◽  
Md Simulations ◽  
Data Bank ◽  
Structural Heterogeneity ◽  
Histone Variants ◽  
Conformational Space ◽  
Dynamics Simulation ◽  
Nucleosome Core

Background: Nucleosomes are basic units of chromatin organization, resembling spools with ~150 base pairs of DNA wrapped around the octamer of histone proteins. They play a crucial role in chromatin compactization and gene expression. Currently, there are more than 340 structures of nucleosomes and their complexes with proteins in the protein data bank, 159 of them are made with cryoEM, 60 of those in 2020 and later. It is clear that cryoEM will soon yield even more structures of nucleosomes with different histone variants, mutations, DNA sequences, and interacting proteins. Despite the variety, the majority of the aforementioned structures look very similar. This is due to the fact that most of the models are built on the basis of very similar crystal structures. However, the dynamics of nucleosomes are crucial for understanding the mechanisms that govern the chromatin functions. Computational methods can supplement experimental approaches and recreate the dynamic conformational landscape of nucleosomes from initial static structures. We present an all-atom molecular dynamics simulation of nucleosome core particles at a record timescale of 15 microseconds. Methods: All-atom MD simulations were performed using GROMACS 2018 with AMBER ff14SB force field with parmbsc1 DNA and CUFIX ion parameters. Crystal structures with PDB IDs 1KX5 and 3LZ0 were used. Analysis was performed with custom-developed python scripts based on MDAnalysis and 3DNA. Models of chromatin fibers were built by connecting random snapshots from MD trajectories with straight linker segments of B-DNA of different lengths. Results: We observed the inner dynamics of histone octamer, which covers the conformational space of the most deformed structures reported by cryoEM. We showed that histone dynamics play important role in DNA mobility, allowing for twist-defects propagation. Conclusion: We observed unprecedented unwrapping of nucleosomal DNA with truncated histone tails. Through multi-scale modeling, we showed that such unwrapping alone is crucial for nucleosomal fibers geometry and elastic properties.

scholarly journals Mechanism for the Unfolding of the TOP7 Protein in Steered Molecular Dynamics Simulations as Revealed by Mutual Information Analysis

2021 ◽  
Vol 8 ◽  
Author(s):  
Ognjen Perišić ◽  
Willy Wriggers
Keyword(s):  
Molecular Dynamics ◽  
Mutual Information ◽  
Novel Mutation ◽  
Steered Molecular Dynamics ◽  
Conformational Space ◽  
Statistical Dependence ◽  
Mechanical Resistance ◽  
The Stability ◽  
Dynamics Simulations ◽  
Mutual Information Analysis

We employed mutual information (MI) analysis to detect motions affecting the mechanical resistance of the human-engineered protein Top7. The results are based on the MI analysis of pair contact correlations measured in steered molecular dynamics (SMD) trajectories and their statistical dependence on global unfolding. This study is the first application of the MI analysis to SMD forced unfolding, and we furnish specific SMD recommendations for the utility of parameters and options in the TimeScapes package. The MI analysis provided a global overview of the effect of perturbation on the stability of the protein. We also employed a more conventional trajectory analysis for a detailed description of the mechanical resistance of Top7. Specifically, we investigated 1) the hydropathy of the interactions of structural segments, 2) the H2O concentration near residues relevant for unfolding, and 3) the changing hydrogen bonding patterns and main chain dihedral angles. The results show that the application of MI in the study of protein mechanical resistance can be useful for the engineering of more resistant mutants when combined with conventional analysis. We propose a novel mutation design based on the hydropathy of residues that would stabilize the unfolding region by mimicking its more stable symmetry mate. The proposed design process does not involve the introduction of covalent crosslinks, so it has the potential to preserve the conformational space and unfolding pathway of the protein.

Improved Sampling Strategies for Protein Model Refinement based on Molecular Dynamics Simulation

2020 ◽  
Author(s):  
Lim Heo ◽  
Collin Arbour ◽  
Michael Feig
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Structure Prediction ◽  
Protein Structures ◽  
Conformational Space ◽  
Dynamics Simulation ◽  
Model Refinement ◽  
Protein Model ◽  
Lower Accuracy ◽  
Simulation Based

Protein structures provide valuable information for understanding biological processes. Protein structures can be determined by experimental methods such as X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, or cryogenic electron microscopy. As an alternative, in silico methods can be used to predict protein structures. Those methods utilize protein structure databases for structure prediction via template-based modeling or for training machine-learning models to generate predictions. Structure prediction for proteins distant from proteins with known structures often results in lower accuracy with respect to the true physiological structures. Physics-based protein model refinement methods can be applied to improve model accuracy in the predicted models. Refinement methods rely on conformational sampling around the predicted structures, and if structures closer to the native states are sampled, improvements in the model quality become possible. Molecular dynamics simulations have been especially successful for improving model qualities but although consistent refinement can be achieved, the improvements in model qualities are still moderate. To extend the refinement performance of a simulation-based protocol, we explored new schemes that focus on an optimized use of biasing functions and the application of increased simulation temperatures. In addition, we tested the use of alternative initial models so that the simulations can explore conformational space more broadly. Based on the insight of this analysis we are proposing a new refinement protocol that significantly outperformed previous state-of-the-art molecular dynamics simulation-based protocols in the benchmark tests described here. <br>

Design of potential IKK-β inhibitors using molecular docking and molecular dynamics techniques for their anti-cancer potential

2020 ◽  
Vol 16 ◽  
Author(s):  
Salam Pradeep Singh ◽  
Iftikar Hussain ◽  
Bolin Kumar Konwar ◽  
Ramesh Chandra Deka ◽  
Chingakham Brajakishor Singh
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Md Simulation ◽  
Inflammatory Diseases ◽  
Binding Free Energy ◽  
Anti Cancer ◽  
Dietary Phytochemicals ◽  
Toxicity Analysis ◽  
The Stability ◽  
Stable Trajectory

Aim and Objective: To evaluate a set of seventy phytochemicals for their potential ability to bind the inhibitor of nuclear factor kappaB kinase beta (IKK-β) which is a prime target for cancer and inflammatory diseases. Materials and Methods: Seventy phytochemicals were screened against IKK-β enzyme using DFT-based molecular docking technique and the top docking hits were carried forward for molecular dynamics (MD) simulation protocols. The adme-toxicity analysis was also carried out for the top docking hits. Results: Sesamin, matairesinol and resveratrol were found to be the top docking hits with a total score of -413 kJ/mol, -398.11 kJ/mol and 266.73 kJ/mol respectively. Glu100 and Gly102 were found to be the most common interacting residues. The result from MD simulation observed a stable trajectory with a binding free energy of -107.62 kJ/mol for matairesinol, -120.37 kJ/mol for sesamin and -40.56 kJ/mol for resveratrol. The DFT calculation revealed the stability of the compounds. The ADME-Toxicity prediction observed that these compounds fall within the permissible area of Boiled-Egg and it does not violate any rule for pharmacological criteria, drug-likeness etc. Conclusion: The study interprets that dietary phytochemicals are potent inhibitors of IKK-β enzyme with favourable binding affinity and less toxic effects. In fact, there is a gradual rise in the use of plant-derived molecules because of its lesser side effects compared to chemotherapy. The study has also provided an insight by which the phytochemicals inhibited the IKK-β enzyme. The investigation would also provide in understanding the inhibitory mode of certain dietary phytochemicals in treating cancer.

Binding of calcium and lead ions to carboxystarch prepared by action of nitrogen dioxide on native starch and its 2,3-dialdehyde derivatives

1986 ◽  
Vol 51 (6) ◽  
pp. 1340-1351 ◽  
Author(s):  
Rudolf Kohn ◽  
Karol Tihlárik
Keyword(s):  
Nitrogen Dioxide ◽  
Alkaline Medium ◽  
Binding Capacity ◽  
Lead Ions ◽  
Carbonyl Groups ◽  
Weakly Alkaline ◽  
Exchange Cations ◽  
Counter Ions ◽  
The Stability ◽  
Derivatives Of

The binding of calcium and lead ions to carboxy derivatives of starch prepared by allowing nitrogen dioxide to act on native maize starch (procedure A) and on starch 2,3-dialdehyde derivatives of degrees of oxidation DO(d.a.) ≥ 0.94 (procedure B) was studied. The carboxy group content of the samples in the H+ form was 4.6 - 12.1 mmol g-1. The effect of alkaline medium on the stability of the carboxy derivatives and on their ability to bind and exchange cations was examined. The Ca2+ → 2K+ exchange was evaluated in terms of the decrease in the electrostatic free enthalpy Δ(Gel/N)KCa, determined by alkalimetric potentiometric titrations, and the binding of Pb2+ ions was evaluated in terms of the activity of the Pb2+ counter-ions determined in suspensions of Pb salts of the carboxy derivatives by means of an ion specific electrode. The IR and CD spectra revealed that the carboxystarch preparations obtained by procedure A contained, in addition to free carboxy groups, a considerable amount of carbonyl groups. During the conversion of the latter groups to the former, even in a weakly alkaline medium, the carboxy derivatives undergo an appreciable degradation and lose, to a great extent, their ability to bind and exchange cations. Procedure B, on the other hand, leads to highly selective starch and amylose carboxy derivatives, exhibiting a small amount of carbonyl groups and featuring a relative stability towards alkaline medium; their binding capacity is as high as 12 milliequivalents of cations per g of sample.

Radiation Effects on Hollandite Ceramics developed for Radioactive Cesium Immobilization

2003 ◽  
Vol 792 ◽  
Author(s):  
V. Aubin ◽  
D. Caurant ◽  
D. Gourier ◽  
N. Baffier ◽  
S. Esnouf ◽  
...  
Keyword(s):  
Radiation Effects ◽  
Liquid Waste ◽  
Fission Products ◽  
Radioactive Cesium ◽  
Radioactive Liquid Waste ◽  
Epr Spectrum ◽  
Paramagnetic Resonance ◽  
Γ Radiation ◽  
The Stability ◽  
High Level

ABSTRACTProgress on separating the long-lived fission products from the high level radioactive liquid waste (HLW) has led to the development of specific host matrices, notably for the immobilization of cesium. Hollandite (nominally BaAl2Ti6O16), one of the main phases constituting Synroc, receives renewed interest as specific Cs-host wasteform. The radioactive cesium isotopes consist of short-lived Cs and Cs of high activities and Cs with long lifetime, all decaying according to Cs+→Ba2++e- (β) + γ. Therefore, Cs-host forms must be both heat and (β,γ)-radiation resistant. The purpose of this study is to estimate the stability of single phase hollandite under external β and γ radiation, simulating the decay of Cs. A hollandite ceramic of simple composition (Ba1.16Al2.32Ti5.68O16) was essentially irradiated by 1 and 2.5 MeV electrons with different fluences to simulate the β particles emitted by cesium. The generation of point defects was then followed by Electron Paramagnetic Resonance (EPR). All these electron irradiations generated defects of the same nature (oxygen centers and Ti3+ ions) but in different proportions varying with electron energy and fluence. The annealing of irradiated samples lead to the disappearance of the latter defects but gave rise to two other types of defects (aggregates of light elements and titanyl ions). It is necessary to heat at relatively high temperature (T=800°C) to recover an EPR spectrum similar to that of the pristine material. The stability of hollandite phase under radioactive cesium irradiation during the waste storage is discussed.

scholarly journals On the Use of the Discrete Constant pH Molecular Dynamics to Describe the Conformational Space of Peptides

Polymers ◽  
2020 ◽  
Vol 13 (1) ◽  
pp. 99
Author(s):  
Cristian Privat ◽  
Sergio Madurga ◽  
Francesc Mas ◽  
Jaime Rubio-Martínez
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Md Simulations ◽  
Point Of View ◽  
Conformational Space ◽  
Conformational Sampling ◽  
Protonation State ◽  
Constant Ph ◽  
Biochemical Systems ◽  
Constant Ph Molecular Dynamics

Solvent pH is an important property that defines the protonation state of the amino acids and, therefore, modulates the interactions and the conformational space of the biochemical systems. Generally, this thermodynamic variable is poorly considered in Molecular Dynamics (MD) simulations. Fortunately, this lack has been overcome by means of the Constant pH Molecular Dynamics (CPHMD) methods in the recent decades. Several studies have reported promising results from these approaches that include pH in simulations but focus on the prediction of the effective pKa of the amino acids. In this work, we want to shed some light on the CPHMD method and its implementation in the AMBER suitcase from a conformational point of view. To achieve this goal, we performed CPHMD and conventional MD (CMD) simulations of six protonatable amino acids in a blocked tripeptide structure to compare the conformational sampling and energy distributions of both methods. The results reveal strengths and weaknesses of the CPHMD method in the implementation of AMBER18 version. The change of the protonation state according to the chemical environment is presumably an improvement in the accuracy of the simulations. However, the simulations of the deprotonated forms are not consistent, which is related to an inaccurate assignment of the partial charges of the backbone atoms in the CPHMD residues. Therefore, we recommend the CPHMD methods of AMBER program but pointing out the need to compare structural properties with experimental data to bring reliability to the conformational sampling of the simulations.

scholarly journals High-resolution mining of the SARS-CoV-2 main protease conformational space: supercomputer-driven unsupervised adaptive sampling

2021 ◽  
Author(s):  
Théo Jaffrelot Inizan ◽  
Frédéric Célerse ◽  
Olivier Adjoua ◽  
Dina El Ahdab ◽  
Luc-Henri Jolly ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
High Resolution ◽  
Adaptive Sampling ◽  
Force Fields ◽  
Sampling Strategy ◽  
Md Simulations ◽  
Conformational Space ◽  
Many Body ◽  
Polarizable Force Fields ◽  
Main Protease

We provide an unsupervised adaptive sampling strategy capable of producing μs-timescale molecular dynamics (MD) simulations of large biosystems using many-body polarizable force fields (PFFs).

scholarly journals Computing the Exact Number of Similarity Classes in the Longest Edge Bisection of Tetrahedra

Mathematics ◽  
2021 ◽  
Vol 9 (12) ◽  
pp. 1447
Author(s):  
Jose P. Suárez ◽  
Agustín Trujillo ◽  
Tania Moreno
Keyword(s):  
Data Structure ◽  
Stability Condition ◽  
Open Problem ◽  
Integer Arithmetic ◽  
Exact Number ◽  
Similarity Class ◽  
The Stability ◽  
High Level ◽  
The Cost

Showing whether the longest-edge (LE) bisection of tetrahedra meshes degenerates the stability condition or not is still an open problem. Some reasons, in part, are due to the cost for achieving the computation of similarity classes of millions of tetrahedra. We prove the existence of tetrahedra where the LE bisection introduces, at most, 37 similarity classes. This family of new tetrahedra was roughly pointed out by Adler in 1983. However, as far as we know, there has been no evidence confirming its existence. We also introduce a new data structure and algorithm for computing the number of similarity tetrahedral classes based on integer arithmetic, storing only the square of edges. The algorithm lets us perform compact and efficient high-level similarity class computations with a cost that is only dependent on the number of similarity classes.

Sign in / Sign up

Export Citation Format

Share Document