keyword
MENU ▼
Read by QxMD icon Read
search

free-energy

keyword
https://www.readbyqxmd.com/read/28732036/an-accurate-coarse-grained-model-for-chitosan-polysaccharides-in-aqueous-solution
#1
Levan Tsereteli, Andrea Grafmüller
Computational models can provide detailed information about molecular conformations and interactions in solution, which is currently inaccessible by other means in many cases. Here we describe an efficient and precise coarse-grained model for long polysaccharides in aqueous solution at different physico-chemical conditions such as pH and ionic strength. The Model is carefully constructed based on all-atom simulations of small saccharides and metadynamics sampling of the dihedral angles in the glycosidic links, which represent the most flexible degrees of freedom of the polysaccharides...
2017: PloS One
https://www.readbyqxmd.com/read/28731682/cold-adaptation-of-triosephosphate-isomerase
#2
Johan Åqvist
The main problem for enzymes from psychrophilic species, that need to work near the freezing point of liquid water, is the exponential decay of reaction rates as the temperature is lowered. Cold-adapted enzymes have solved this problem by shifting the activation enthalpy-entropy balance for the catalyzed reaction compared to their mesophilic orthologs. To understand the structural basis of this universal feature it is necessary to examine pairs of such orthologous enzymes, with known 3D structures, at the microscopic level...
July 21, 2017: Biochemistry
https://www.readbyqxmd.com/read/28731091/developing-force-fields-when-experimental-data-is-sparse-amber-gaff-compatible-parameters-for-inorganic-and-alkyl-oxoanions
#3
Sadra Kashefolgheta, Ana Vila Verde
We present a set of Lennard-Jones parameters for classical, all-atom models of acetate and various alkylated and non-alkylated forms of sulfate, sulfonate and phosphate ions, optimized to reproduce their interactions with water and with the physiologically relevant sodium, ammonium and methylammonium cations. The parameters are internally consistent and are fully compatible with the Generalized Amber Force Field (GAFF), the AMBER force field for proteins, the accompanying TIP3P water model and the sodium model of Joung and Cheatham...
July 21, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28730879/rgrna-prediction-of-rna-secondary-structure-based-on-replacement-and-growth-of-stems
#4
Jin Li, Chengzhen Xu, Hong Liang, Wang Cong, Ying Wang, Kuan Luan, Yunlong Liu
Owing to their structural diversity, RNAs perform many diverse biological functions in the cell. RNA secondary structure is thus important for predicting RNA function. Here, we propose a new combinatorial optimization algorithm, named RGRNA, to improve the accuracy of predicting RNA secondary structure. Following the establishment of a stempool, the stems are sorted by length, and chosen from largest to smallest. If the stem selected is the true stem, the secondary structure of this stem when combined with another stem selected at random will have low free energy, and the free energy will tend to gradually diminish...
July 21, 2017: Computer Methods in Biomechanics and Biomedical Engineering
https://www.readbyqxmd.com/read/28730429/a-new-method-to-predict-ion-effects-in-rna-folding
#5
Li-Zhen Sun, Shi-Jie Chen
The strong interaction between metal ions in solution and highly charged RNA molecules is critical for RNA structure formation and stabilization. Metal ions binding to RNA can induce RNA structural changes that are important for RNA cellular functions. Therefore, quantitative modeling of the ion effects is essential for RNA structure prediction and RNA-based molecular design. Recently, inspired by the increasing experimental evidence that supports the importance of ion correlation and fluctuation in ion-RNA interactions, we developed a new computational model, Monte Carlo Tightly Bound Ion (MCTBI) model...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28728667/a-comparison-between-liquid-drops-and-solid-particles-in-partial-wetting
#6
REVIEW
Antonio Stocco, Maurizio Nobili
In this critical review we compare two geometries in partial wetting: a liquid drop on a planar substrate and a spherical particle at a planar liquid interface. We show that this comparison is far from being trivial even if the same physical interactions are at play in both geometries. Similarities and differences in terms of free energies and frictions will be discussed. Contact angle hysteresis, the impact of surface roughness and line pinning on wetting will be described and compared to selected experimental findings...
July 1, 2017: Advances in Colloid and Interface Science
https://www.readbyqxmd.com/read/28728523/structural-insights-into-the-binding-of-small-ligand-molecules-to-a-g-quadruplex-dna-located-in-the-hiv-1-promoter
#7
Petar M Mitrasinovic
Targeting guanine (G)-rich DNA sequences, folded into non-canonical G-quadruplex (G4) structures, by small ligand molecules is a promising strategy for gene therapy of various diseases. There is experimental proposal that, among eight studied ligands, nitidine chloride - NC and a benzo phenanthridine derivative - BPD have the highest binding affinities for such a sequence (5'-T(1)G(2)G(3)C(4)C(5)T(6)G(7)G(8)G(9)C(10)G(11)G(12)G(13)A(14)C(15)T(16)G(17)G(18)G(19)-3') in the HIV-1 promoter, indicating that an anti-HIV-1 prodrug may regulate the expression of the promoter...
July 20, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28727767/exploring-the-binding-pathways-of-the-14-3-3%C3%AE-protein-structural-and-free-energy-profiles-revealed-by-hamiltonian-replica-exchange-molecular-dynamics-with-distancefield-distance-restraints
#8
Gabor Nagy, Chris Oostenbrink, Jozef Hritz
The 14-3-3 protein family performs regulatory functions in eukaryotic organisms by binding to a large number of phosphorylated protein partners. Whilst the binding mode of the phosphopeptides within the primary 14-3-3 binding site is well established based on the crystal structures of their complexes, little is known about the binding process itself. We present a computational study of the process by which phosphopeptides bind to the 14-3-3ζ protein. Applying a novel scheme combining Hamiltonian replica exchange molecular dynamics and distancefield restraints allowed us to map and compare the most likely phosphopeptide-binding pathways to the 14-3-3ζ protein...
2017: PloS One
https://www.readbyqxmd.com/read/28727426/fully-atomistic-a%C3%AE-40-and-a%C3%AE-42-oligomers-in-water-observation-of-pore-like-conformations
#9
Matthew John Voelker, Bogdan Barz, Brigita Urbanc
Oligomers formed by amyloid β-protein (Aβ) are central to Alzheimer's disease (AD) pathology, yet their structure remains elusive. Of the two predominant Aβ alloforms, Aβ40 and Aβ42, the latter is more strongly associated with AD. Here, we structurally characterized Aβ40 and Aβ42 monomers through pentamers which were converted from previously derived coarse-grained (DMD4B-HYDRA) simulations into all-atom conformations and subjected to explicit-solvent MD. Free energy landscapes revealed that structural differences between Aβ40 and Aβ42 conformations increase with oligomer order up to trimers...
July 20, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28723223/free-energy-of-binding-and-mechanism-of-interaction-for-the-meevd-tpr2a-peptide-protein-complex
#10
Mauro Lapelosa
The association between the MEEVD C-terminal peptide from the heat shock protein 90 (Hsp90) and tetratricopeptide repeat A (TPR2A) domain of the heat shock organizing protein (Hop) is a useful prototype to study the fundamental molecular details about the Hop-Hsp90 interaction. We study here the mechanism of binding/unbinding, and compute the standard binding free energy and potential of mean force for the association of the MEEVD peptide to the TPR2A domain using the Adaptive Biasing Force (ABF) methodology...
July 19, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28723106/proteins-breaking-bad-a-free-energy-perspective
#11
Jessica Valle-Orero, Rafael Tapia-Rojo, Edward C Eckels, Jaime Andres Rivas-Pardo, Ionel Popa, Julio M Fernandez
Protein ageing may manifest as a mechanical disease that compromises tissue elasticity. As proved recently, while proteins respond to changes in force with an instantaneous elastic recoil followed by a folding contraction, aged proteins break bad, becoming unstructured polymers. Here, we explain this phenomenon in the context of a free energy model, predicting the changes in the folding landscape of proteins upon oxidative ageing. Our findings validate that protein folding under force is constituted by two separable components, polymer properties and hydrophobic collapse, and demonstrate that the latter becomes irreversibly blocked by oxidative damage...
July 19, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28723063/using-cooperatively-folded-peptides-to-measure-interaction-energies-and-conformational-propensities
#12
Maziar S Ardejani, Evan T Powers, Jeffery W Kelly
The rates and equilibria of the folding of biopolymers are determined by the conformational preferences of the subunits that make up the sequence of the biopolymer and by the interactions that are formed in the folded state in aqueous solution. Because of the centrality of these processes to life, quantifying conformational propensities and interaction strengths is vitally important to understanding biology. In this Account, we describe our use of peptide model systems that fold cooperatively yet are small enough to be chemically synthesized to measure such quantities...
July 19, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28722064/effect-of-alkyl-branches-on-the-thermal-stability-of-quaternary-ammonium-cations-in-organic-electrolytes-for-electrochemical-double-layer-capacitors
#13
Yong Nam Ahn, Sung Hoon Lee, Goo Soo Lee, Hyunbin Kim
Quaternary ammoniums are cations having widespread use in organic electrolytes for high performance electrochemical double layer capacitors (EDLCs) due to their various advantages such as high electrochemical stability and inexpensive production cost. However, the decomposition of quaternary ammoniums via Hofmann elimination hinders their applications for EDLCs operating at elevated temperatures. This study systematically investigates the reactivity of four different quaternary ammoniums (tetraethyl-, triethylmethyl-, diethyldimethyl-, and trimethylethyl-ammonium) in EDLC by utilizing density functional theory calculations and Brownian dynamics simulations complemented with molecular dynamics simulations...
July 19, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28721412/effect-of-ligand-binding-on-a-protein-with-a-complex-folding-landscape
#14
Hisham Mazal, Haim Aviram, Inbal Riven, Gilad Haran
Ligand binding to a protein can stabilize it significantly against unfolding. The variation of the folding free energy, ΔΔG(0), due to ligand binding can be derived from a simple reaction scheme involving exclusive binding to the native state. One obtains the following expression: , where Kd is the ligand dissociation constant and L is its concentration, R is the universal gas constant and T is the temperature. This expression has been shown to correctly describe experimental results on multiple proteins...
July 19, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28720769/concentration-dependent-binding-of-small-ligands-to-multiple-saturable-sites-in-membrane-proteins
#15
Letícia Stock, Juliana Hosoume, Werner Treptow
Membrane proteins are primary targets for most therapeutic indications in cancer and neurological diseases, binding over 50% of all known small molecule drugs. Understanding how such ligands impact membrane proteins requires knowledge on the molecular structure of ligand binding, a reasoning that has driven relentless efforts in drug discovery and translational research. Binding of small ligands appears however highly complex involving interaction to multiple transmembrane protein sites featuring single or multiple occupancy states...
July 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28720698/catalysis-and-chemical-mechanisms-of-calcite-dissolution-in-seawater
#16
Adam V Subhas, Jess F Adkins, Nick E Rollins, John Naviaux, Jonathan Erez, William M Berelson
Near-equilibrium calcite dissolution in seawater contributes significantly to the regulation of atmospheric [Formula: see text] on 1,000-y timescales. Despite many studies on far-from-equilibrium dissolution, little is known about the detailed mechanisms responsible for calcite dissolution in seawater. In this paper, we dissolve (13)C-labeled calcites in natural seawater. We show that the time-evolving enrichment of [Formula: see text] in solution is a direct measure of both dissolution and precipitation reactions across a large range of saturation states...
July 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28720500/essential-slow-degrees-of-freedom-in-protein-surface-simulations-a-metadynamics-investigation
#17
Arushi Prakash, K G Sprenger, Jim Pfaendtner
Many proteins exhibit strong binding affinities to surfaces, with binding energies much greater than thermal fluctuations. When modelling these protein-surface systems with classical molecular dynamics (MD) simulations, the large forces that exist at the protein/surface interface generally confine the system to a single minimum. Exploring the full conformational space of the protein, especially finding other stable structures, becomes prohibitively expensive. Coupling MD simulations with metadynamics (enhanced sampling) has fast become a common method for sampling the adsorption of such proteins...
July 15, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28719051/the-binding-mechanism-between-azoles-and-fgcyp51b-sterol-14%C3%AE-demethylase-of-fusarium-graminearum
#18
Hengwei Qian, Meilin Duan, Xiaomei Sun, Mengyu Chi, Ying Zhao, Wenxing Liang, Juan Du, Jinguang Huang, Baodu Li
BACKGROUND: Fusarium graminearum is the main pathogen of Fusarium Head Blight (FHB), a worldwide plant disease and one of the major wheat diseases in China. The control of the FHB is mainly dependent on the application of DMIs fungicides. Fungal sterol 14α-demethylase enzymes (CYP51) are the main target for DMIs fungicides. In order to investigate the binding mechanism between azoles and CYP51B in F.graminearum, the molecular modeling study and biological evaluation were performed. RESULTS: Firstly, the homology model based on the crystal structure of Aspergillus fumigatus was built...
July 18, 2017: Pest Management Science
https://www.readbyqxmd.com/read/28718973/constructing-a-multidimensional-free-energy-surface-like-a-spider-weaving-a-web
#19
Changjun Chen
Complete free energy surface in the collective variable space provides important information of the reaction mechanisms of the molecules. But, sufficient sampling in the collective variable space is not easy. The space expands quickly with the number of the collective variables. To solve the problem, many methods utilize artificial biasing potentials to flatten out the original free energy surface of the molecule in the simulation. Their performances are sensitive to the definitions of the biasing potentials...
July 18, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28718930/genesis-1-1-a-hybrid-parallel-molecular-dynamics-simulator-with-enhanced-sampling-algorithms-on-multiple-computational-platforms
#20
Chigusa Kobayashi, Jaewoon Jung, Yasuhiro Matsunaga, Takaharu Mori, Tadashi Ando, Koichi Tamura, Motoshi Kamiya, Yuji Sugita
GENeralized-Ensemble SImulation System (GENESIS) is a software package for molecular dynamics (MD) simulation of biological systems. It is designed to extend limitations in system size and accessible time scale by adopting highly parallelized schemes and enhanced conformational sampling algorithms. In this new version, GENESIS 1.1, new functions and advanced algorithms have been added. The all-atom and coarse-grained potential energy functions used in AMBER and GROMACS packages now become available in addition to CHARMM energy functions...
July 18, 2017: Journal of Computational Chemistry
keyword
keyword
74789
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"