Read by QxMD icon Read

Molecular dynamics simulation free energy

Snehasis Bhunia, Ajeet Singh, Animesh K Ojha
Complexes of the dipeptide phenylalanine-phenylalanine (Phe-Phe) with divalent metal cations (Cu(2+), Zn(2+), Ca(2+) and Ba(2+)) were studied at the B3LYP and MP2 levels of theory with the basis sets 6-311++G(d,p) and 6-31 + G(d) in the gas phase. The relative energies of these complexes indicated that cation-π bidentate/tridentate conformations are more favourable than other conformations with uncoordinated rings. These findings were confirmed by the calculated values of thermodynamic parameters such as the Gibbs free energy...
March 2017: Journal of Molecular Modeling
Sonanki Keshri, B L Tembe
Molecular dynamics simulations of fullerene and fullerols [C60(OH)n, where n = 2-30] in aqueous solutions have been performed for the purpose of obtaining a detailed understanding of the structural and dynamic properties of these nanoparticles in water. The structures, dynamics and hydration free energies of the solute molecules in water have been analysed. Radial distribution functions, spatial density distribution functions and hydrogen bond analyses are employed to characterize the solvation shells of water around the central solute molecules...
February 21, 2017: Journal of Chemical Physics
Xueming Tang, Weizhong Zou, Peter H Koenig, Shawn D McConaughy, Michael R Weaver, David Michael Eike, Michael J Schmidt, Ronald G Larson
We link micellar structures to rheological properties for two surfactant body-wash formulations at various concentrations of salts and perfume raw materials (PRMs) using molecular simulations and micellar-scale modeling as well as traditional surfactant packing arguments. The two body washes, named BW-1EO and BW-3EO, are composed of sodium lauryl ethylene glycol ether sulfate (SLEnS, where n is the average number of ethylene glycol repeat units), cocamidopropyl betaine (CAPB), ACCORD (which is a mixture of six PRMs), and NaCl salt...
February 22, 2017: Journal of Physical Chemistry. B
Yushu Chen, Magali Duvail, Philippe Guilbaud, Jean-François Dufrêche
Molecular complexes formed in the organic phase during solvent extraction may self-assemble as reverse micelles, and therefore induce a supramolecular organization of this phase. In most of the cases, water molecules play an essential role in the organization of this non polar medium. The aim of this work is to investigate the speciation of the aggregates formed in the organic phase during solvent extraction, and especially to assess their stability as a function of the number of water molecules included in their polar core...
February 22, 2017: Physical Chemistry Chemical Physics: PCCP
Hideaki Takahashi, Satoru Umino, Yuji Miki, Ryosuke Ishizuka, Shu Maeda, Akihiro Morita, Makoto Suzuki, Nobuyuki Matubayasi
Hydrolysis of adenosine triphosphate (ATP) is the "energy source" for a variety of biochemical processes. In the present work, we address key features of ATP hydrolysis: the relatively moderate value (about -10 kcal/mol) of the standard free energy ΔGhyd of reaction and the insensitivity of ΔGhyd to the number of excess electrons on ATP. We conducted quantum mechanical/molecular mechanical (QM/MM) simulation combined with the energy-representation theory of solutions to analyze the electronic-state and solvation contributions to ΔGhyd...
February 21, 2017: Journal of Physical Chemistry. B
Emilia Pecora de Barros, Robert D Malmstrom, Kimya Nourbakhsh, Jason Cruz Del Rio, Alexandr P Kornev, Susan S Taylor, Rommie E Amaro
Close-range electrostatic interactions that form salt bridges are key components of protein stability. Here we investigate the role of these charged interactions in modulating the allosteric activation of Protein Kinase A (PKA) via computational and experimental mutational studies on a conserved basic patch located in the regulatory subunit's B/C helix. Molecular dynamics simulations evidenced the presence of an extended network of fluctuating salt bridges spanning the helix and connecting the two cAMP binding domains in its extremities...
February 21, 2017: Biochemistry
Lulu Yang, Wu Yang, Zhiwei Wu, Zhongsheng Yi
Three hydroxylated polybrominated diphenyl ethers (OH-PBDEs), 3-OH-BDE-47, 5-OH-BDE-47, and 6-OH-BDE-47, were selected to investigate the interactions between OH-PBDEs with human serum albumin (HSA) under physiological conditions. The observed fluorescence quenching can be attributed to the formation of complexes between HSA and OH-PBDEs. The thermodynamic parameters at different temperatures indicate that the binding was caused by hydrophobic forces and hydrogen bonds. Molecular modeling and three-dimensional fluorescence spectrum showed conformational and microenvironmental changes in HSA...
February 21, 2017: Luminescence: the Journal of Biological and Chemical Luminescence
Huiming Cao, Yuzhen Sun, Ling Wang, Chunyan Zhao, Jianjie Fu, Aiqian Zhang
Polybrominated diphenyl ethers (PBDEs), one typical type of persistent environmental contaminant, have toxicological effects such as disrupting thyroid homeostasis in the human body. The high binding affinities of hydroxylated metabolites of PBDEs (OH-PBDEs) with transthyretin (TTR) were considered to be one major reason for their extraordinary capacity of passing through the blood-brain barrier via competitive thyroid hormone (T4) transport protein binding. Recent findings showed that sulfated PBDEs can be formed in human liver cytosol as phase-II metabolites...
February 20, 2017: Molecular BioSystems
Joshua E Condon, Tyler B Martin, Arthi Jayaraman
Using atomistic and coarse-grained molecular dynamics (MD) simulations, we explain the shifts in lower critical solution temperature (LCST)-like phase transitions exhibited by elastin-like peptides (ELPs) upon conjugation to other macromolecules (e.g. collagen-like peptides or CLPs). First, using atomistic simulations, we study ELP oligomers with the sequence (VPGFG)6 in explicit water, and characterize the LCST-like transition temperature as one at which the ELP oligomers undergo a change in "hydration state"...
February 20, 2017: Soft Matter
Martiniano Bello, Lucia Basilio-Antonio, Jonathan Fragoso-Vázquez, Anaguiven Avalos-Soriano, José Correa-Basurto
Pancreatic lipase (PL) is a primary lipase critical for triacylglyceride digestion in humans and is considered as a promising target for the treatment of obesity. Although the current synthetic drugs available for treating obesity have been demonstrated to be effective in inhibiting PL, their prolonged usage results in severe side effects. Based on this argument, in this study, we evaluated the structural and energetic features linked to molecular recognition between two well-known PL inhibitors, orlistat (ORL, synthetic inhibitor) and (-)-epigallocatechin gallate (EGCG, natural inhibitor) and PL through molecular dynamics simulations and free energy calculations of ORL and EGCG at the PL binding site when it is isolated (PL) from the heterodimer complex, forming the heterodimer complex with colipase (PLCL) and lacking structural calcium...
February 16, 2017: International Journal of Biological Macromolecules
Greg Starek, J Alfredo Freites, Simon Bernèche, Douglas J Tobias
We used targeted molecular dynamics, informed by experimentally determined inter-atomic distances defining the pore region of open and closed states of the KvAP voltage-gated potassium channel, to generate a gating pathway of the pore domain in the absence of the voltage-sensing domains. We then performed umbrella sampling simulations along this pathway to calculate a potential of mean force that describes the free energy landscape connecting the closed and open conformations of the pore domain. The resulting energetic landscape displays three minima, corresponding to stable open, closed, and intermediate conformations with roughly similar stabilities...
February 16, 2017: Journal of Computational Chemistry
A J Alvarez-Socorro, M G Clerc, G González-Cortés, M Wilson
Multistable systems exhibit a rich front dynamics between equilibria. In one-dimensional scalar gradient systems, the spread of the fronts is proportional to the energy difference between equilibria. Fronts spreading proportionally to the energetic difference between equilibria is a characteristic of one-dimensional scalar gradient systems. Based on a simple nonvariational bistable model, we show analytically and numerically that the direction and speed of front propagation is led by nonvariational dynamics...
January 2017: Physical Review. E
Yan-Jun Zhang, Jing-Na Ding, Hui Zhong, Ju-Guang Han
Multifunctional viral protein (VP35) encoded by the highly pathogenic Ebola viruses (EBOVs) can antagonize host double-stranded RNA (dsRNA) sensors and immune response because of the simultaneous recognition of dsRNA backbone and blunt ends. Mutation of select hydrophobic conserved basic residues within the VP35 inhibitory domain (IID) abrogates its dsRNA-binding activity, and impairs VP35-mediated interferon (IFN) antagonism. Herein the detailed binding mechanism between dsRNA and WT, single mutant, and double mutant were investigated by all-atom molecular dynamics (MD) simulation and binding energy calculation...
February 16, 2017: Proteins
Jerome Cuny, Kseniia Korchagina, Chemseddine Menakbi, Tzonka Mineva
Application of ab initio molecular dynamics to study free energy surfaces (FES) is still not commonly performed because of the extensive sampling required. Indeed, it generally necessitates computationally costly simulations of more than several hundreds of picoseconds. To achieve such studies, efficient density functional theory (DFT) formalisms, based on various levels of approximate computational schemes, have been developed, and provide a good alternative to commonly used DFT implementations. We report benchmark results on the conformational change FES of alanine dipeptide obtained with auxiliary density functional theory (ADFT) and second- and third-order density functional tight-binding (DFTB) methods coupled to metadynamics simulations...
March 2017: Journal of Molecular Modeling
Vojtech Mlynsky, Giovanni Bussi
Ribonucleic acid (RNA) is involved in many regulatory and catalytic processes in the cell. The function of any RNA molecule is intimately related with its structure. In-line probing experiments provide valuable structural datasets for a variety of RNAs and are used to characterize conformational changes in riboswitches. However, the structural determinants that lead to differential reactivities in unpaired nucleotides have not been investigated yet. In this work we used a combination of theoretical approaches, i...
February 15, 2017: RNA
Davit Hakobyan, Andreas Heuer
Based on all-atom Molecular Dynamics (MD) simulations of a lipid bilayer we present a systematic mapping on a 2D lattice model. Keeping the lipid type and the chain order parameter as key variables we derive a free energy functional, containing the enthalpic interaction of adjacent lipids as well as the tail entropy. The functional form of both functions is explicitly determined for saturated and polyunsaturated lipids. By studying the lattice model via Monte Carlo simulations it is possible to reproduce the temperature dependence of the distribution of order parameters of the pure lipids, including the prediction of the gel transition...
February 14, 2017: Journal of Chemical Physics
Chao E, Baogen Duan, Jin Yu
Nucleotide selection is crucial for transcription fidelity control, in particular, for viral T7 RNA polymerase (RNAP) lack of proofreading activity. It has been recognized that multiple kinetic checkpoints exist prior to full nucleotide incorporation. In this work, we implemented intensive atomistic molecular dynamics (MD) simulations to quantify how strong the nucleotide selection is at the initial checkpoint of an elongation cycle of T7 RNAP. The incoming nucleotides bind into a pre-insertion site where a critical tyrosine residue locates nearby to assist the nucleotide selection...
February 15, 2017: Journal of Physical Chemistry. B
Barbara Gregori, Leonardo Guidoni, Maria Elisa Crestoni, Pedro de Oliveira, Chantal Houée-Levin, Debora Scuderi
The gas-phase structural modifications induced by the oxidation of methionine of two peptides of reverse sequence, methionine-valine (Met-Val) and valine-methionine (Val-Met), have been studied by mass-selected infrared multiple photon dissociation (IRMPD) spectroscopy in the 800-2000 cm-1 fingerprint range at the Centre Laser Infrarouge d'Orsay (CLIO) free electron laser facility. Oxidation has been achieved by •OH radicals generated by γ-radiolysis. IRMPD spectra were interpreted by static and harmonic DFT calculations and Born-Oppenheimer molecular dynamics simulations, employed to take into account all anharmonic and finite temperature effects...
February 14, 2017: Journal of Physical Chemistry. B
Bobo Dang, Rong Shen, Tomoya Kubota, Kalyaneswar Mandal, Francisco Bezanilla, Benoit Roux, Stephen B H Kent
ShK toxin is a cysteine-rich 35-residue protein ion-channel ligand isolated from the sea anemone Stichodactyla helianthus. In this work, we studied the effect of inverting the side chain stereochemistry of individual Thr or Ile residues on the properties of the ShK protein. Molecular dynamics simulations were used to calculate the free energy cost of inverting the side-chain stereochemistry of individual Thr or Ile residues. Guided by the computational results, we used chemical protein synthesis to prepare three ShK polypeptide chain analogues, each containing either an allo-Thr or an allo-Ile residue...
February 14, 2017: Angewandte Chemie
Lara A Patel, James T Kindt
We introduce a global fitting analysis method to obtain free energies of association of non-covalent molecular clusters using equilibrated cluster size distributions from unbiased constant-temperature molecular dynamics (MD) simulations. Because the systems simulated are small enough that the law of mass action does not describe the aggregation statistics, the method relies on iteratively determining a set of cluster free energies that, using appropriately weighted sums over all possible partitions of N monomers into clusters, produces the best-fit size distribution...
February 13, 2017: Journal of Chemical Theory and Computation
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"