Read by QxMD icon Read

Molecular dynamics simulation free energy

Artturi Koivuniemi, Kristiina Takkinen, Tarja Nevanen
Given the increasing exploitation of antibodies in different contexts such as molecular diagnostics and therapeutics, it would be beneficial to unravel the atomistic level properties of antibody-antigen complexes with the help of computational modeling. Thus, here we have studied the feasibility of computational tools to gather atomic scale information regarding the antibody-antigen complexes solely starting from an amino acid sequence. First, we constructed a homology model for the anti-testosterone binding antibody based on the knowledge based classification of complementary determining regions (CDRs) and implicit solvent molecular dynamics simulations...
December 9, 2016: Proteins
Gabriele Cesare Sosso, Sebastiano Caravati, Grant Rotskoff, Suriyanarayanan Vaikuntanathan, Ali A Hassanali
Density fluctuations in liquid water are at the heart of numerous phenomena associated with hydrophobic effects such as protein folding and the interaction between bio-molecules. One of the most fundamental processes in this regard, is the solvation of hydrophobic solutes in water. The vast majority of theoretical and numerical studies examine density fluctuations at the short length-scale focusing exclusively on spherical cavities. In this work, we use both first principles and classical molecular dynamics simulations to demonstrate that density fluctuations in liquid water can deviate significantly from the canonical spherical shapes...
December 9, 2016: Journal of Physical Chemistry. A
Víctor Gómez-González, Borja Docampo-Álvarez, Trinidad Méndez-Morales, Oscar Cabeza, Vladislav B Ivaništšev, Maxim V Fedorov, Luis J Gallego, Luis M Varela
A molecular dynamics study of mixtures of 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIm][BF4]) with magnesium tetrafluoroborate (Mg[BF4]2) confined between two parallel graphene walls is reported. The structure of the system is analyzed by means of ionic density profiles, lateral structure of the first layer close to the graphene surface and angular orientations of imidazolium cations. Free energy profiles for divalent magnesium cations are calculated using two different methods in order to evaluate the height of the potential barriers near the walls, and the results are compared with those of mixtures of the same ionic liquid and a lithium salt (Li[BF4])...
December 9, 2016: Physical Chemistry Chemical Physics: PCCP
Michael Holmboe, Per Larsson, Jamshed Anwar, Christel A S Bergström
We performed molecular dynamics (MD) simulations to obtain insights into the structure and molecular interactions of colloidal structures present in fasted state intestinal fluid. Drug partitioning and interaction were studied with a mixed system of the bile salt taurocholate (TCH) and 1,2-dilinoleoyl-sn-glycero-3-phosphocholine (DLiPC). Spontaneous aggregation of TCH and DLiPC from unconstrained MD simulations at the united-atom level using the Berger/Gromos54A7 force fields demonstrated that intermolecular hydrogen bonding between TCH molecules was an important factor in determining the overall TCH and DLiPC configuration...
December 6, 2016: Langmuir: the ACS Journal of Surfaces and Colloids
Da Wang, Djurre H de Jong, Andreas Rühling, Volker Lesch, Karina Shimizu, Stephanie Wulff, Andreas Heuer, Frank Glorius, Hans-Joachim Galla
4,5-Dialkylated imidazolium lipid salts are a new class of lipid analogues showing distinct biological activities. The potential effects of the imidazolium lipids on artificial lipid membranes and the corresponding membrane interactions was analyzed. Therefore, 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) was employed to create an established lipid monolayer model and a bilayer membrane. Mixed monolayers of DPPC and 4,5-dialkylimidazolium lipids differing by their alkyl chain length (C7, C11, and C15) were characterized by surface pressure-area (π-A) isotherms using a Wilhelmy film balance in combination with epifluorescence microscopy...
December 6, 2016: Langmuir: the ACS Journal of Surfaces and Colloids
Yeonho Song, Ji Hye Lee, Hoon Hwang, George C Schatz, Hyonseok Hwang
Potential of mean force (PMF) profiles and position-dependent diffusion coefficients of Na(+) and K(+) are calculated to elucidate the translocation of ions through a cyclic peptide nanotube, composed of 8 × cyclo[-(d-Leu-Trp)4-] rings, in water and in hydrated DMPC bilayers. The PMF profiles and PMF decomposition analysis for the monovalent cations show that favorable interactions of the cations with the CPN as well as the lipid bilayer and dehydration free energy penalties are two major competing factors which determine the free energy surface for ion transport through CPNs both in water and in lipid bilayers, and that the selectivity of CPNs to cations mainly arises from favorable interaction energies of cations with CPNs and lipid bilayers that are more dominant than the dehydration penalties...
November 23, 2016: Journal of Physical Chemistry. B
Asuka A Orr, Michael M Wördehoff, Wolfgang Hoyer, Phanourios Tamamis
Amyloidogenic proteins amyloid-β peptide (Aβ) and α-synuclein (α-syn) self-assemble into fibrillar amyloid deposits, senile plaques and Lewy bodies, pathological features of Alzheimer's and Parkinson's diseases, respectively. Interestingly, a portion of Alzheimer's disease cases also exhibit aggregation of α-syn into Lewy bodies, and growing evidence also suggests that Aβ and α-syn oligomers are toxic. Therefore, the simultaneous inhibition through sequestration of the two amyloidogenic proteins may constitute a promising therapeutic strategy...
December 9, 2016: Journal of Physical Chemistry. B
Junjie Zou, Benben Song, Carlos Simmerling, Daniel Raleigh
The rational and predictable enhancement of protein stability is an important goal in protein design. Most efforts target the folded state, however stability is the free energy difference between the folded and unfolded states thus both are suitable targets. Strategies directed at the unfolded state usually seek to decrease chain entropy by introducing cross-links or by replacing glycines. Cross-linking has led to mixed results. Replacement of glycine with an l-amino acid, while reducing the entropy of the unfolded state, can introduce unfavorable steric interactions in the folded state, since glycine is often found in conformations that require a positive φ angle such as helical C-capping motifs or type I' and II″ β-turns...
December 7, 2016: Journal of the American Chemical Society
Phuong H Nguyen, Fabio Sterpone, Ramon Pouplana, Philippe Derreumaux, Josep M Campanera
Amyloid beta (Aβ) oligomerization is associated with the origin and progression of Alzheimer's disease (AD). While the A2V mutation enhances aggregation kinetics and toxicity, mixtures of wild-type (WT) and A2V, and also WT and A2T, peptides retard fibril formation and protect against AD. In this study, we simulate the equilibrium ensemble of WT:A2T Aβ40 dimer by means of extensive atomistic replica exchange molecular dynamics and compare our results with previous equivalent simulations of A2V:A2V, WT:WT, and WT:A2V Aβ40 dimers for a total time scale of nearly 0...
December 1, 2016: Journal of Physical Chemistry. B
Ikbae Son, Tigran V Chalikian
We report the first experimental characterization of the full thermodynamic profile for binding of urea to a native protein. We measured the volumetric parameters of lysozyme at pH 7.0 as a function of urea within a temperature range of 18-45 °C. At neutral pH, lysozyme retains its native conformation between 0 and 8 M urea over the entire range of temperatures studied. Consequently, our measured volumetric properties reflect solely the interactions of urea with the native protein and do not involve contributions from urea-induced conformational transitions...
November 29, 2016: Biochemistry
Leila Karami, Ali Akbar Saboury, Elham Rezaee, Sayyed Abbas Tabatabai
The soluble epoxide hydrolase (sEH) enzyme plays an important role in the metabolism of endogenous chemical mediators involved in the regulation of blood pressure and inflammation. Inhibition of sEH provides a new approach to the treatment of inflammation, hypertension and atherosclerosis. In this study, the binding modes and inhibition mechanisms of the new oxadiazole-based amide inhibitors of the human soluble epoxide hydrolase were investigated by molecular docking and molecular dynamics (MD) simulation followed by the MM-GBSA method to calculate the binding free energy of each inhibitor to sEH...
December 7, 2016: European Biophysics Journal: EBJ
Camilo Andrés Mora Osorio, Andrés Fernando González Barrios
BACKGROUND: Calculation of the Gibbs free energy changes of biological molecules at the oil-water interface is commonly performed with Molecular Dynamics simulations (MD). It is a process that could be performed repeatedly in order to find some molecules of high stability in this medium. Here, an alternative method of calculation has been proposed: a group contribution method (GCM) for peptides based on MD of the twenty classic amino acids to obtain free energy change during the insertion of any peptide chain in water-dodecane interfaces...
December 7, 2016: BMC Bioinformatics
Martin J Fossat, Thuy P Dao, Kelly Jenkins, Mariano Dellarole, Yinshan Yang, Scott A McCallum, Angel E Garcia, Doug Barrick, Christian Roumestand, Catherine A Royer
A complete description of the pathways and mechanisms of protein folding requires a detailed structural and energetic characterization of the conformational ensemble along the entire folding reaction coordinate. Simulations can provide this level of insight for small proteins. In contrast, with the exception of hydrogen exchange, which does not monitor folding directly, experimental studies of protein folding have not yielded such structural and energetic detail. NMR can provide residue specific atomic level structural information, but its implementation in protein folding studies using chemical or temperature perturbation is problematic...
December 6, 2016: Biophysical Journal
Kai-Hsin Liou, Dun-Yen Kang, Li-Chiang Lin
Water shortage has become a critical issue. To facilitate the large-scale deployment of reverse-osmosis water desalination to produce fresh water, discovering novel membranes is essential. Here, we computationally demonstrate the great potential of single-walled aluminosilicate nanotubes (AlSiNTs), materials that can be synthesized through scalable methods, in desalination. State-of-the-art molecular dynamics simulations were employed to investigate the desalination performance and structure-performance relationship of AlSiNTs...
November 4, 2016: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
Tiantian Zhang, Tao Wei, Yuanyuan Han, Heng Ma, Mohammadreza Samieegohar, Ping-Wei Chen, Ian Lian, Yu-Hwa Lo
Protein-ligand interaction detection without disturbances (e.g., surface immobilization, fluorescent labeling, and crystallization) presents a key question in protein chemistry and drug discovery. The emergent technology of transient induced molecular electronic spectroscopy (TIMES), which incorporates a unique design of microfluidic platform and integrated sensing electrodes, is designed to operate in a label-free and immobilization-free manner to provide crucial information for protein-ligand interactions in relevant physiological conditions...
November 23, 2016: ACS Central Science
Xian Xiao, Qiang-Hua He, Li-Yan Yu, Song-Qing Wang, Yang Li, Hua Yang, Ai-Hua Zhang, Xiao-Hong Ma, Yu-Jie Peng, Bing Chen
The PTP non-receptor type 4 (PTPN4) is an important regulator protein in learning, spatial memory and cerebellar synaptic plasticity; targeting the PDZ domain of PTPN4 has become as attractive therapeutic strategy for human neuroglioma. Here, we systematically examined the complex crystal structures of PTPN4 PDZ domain with its known peptide ligands; a number of charged amino acid residues were identified in these ligands and in the peptide-binding pocket of PDZ domain, which can constitute a complicated salt-bridge network across the complex interface...
November 30, 2016: Computational Biology and Chemistry
Budheswar Dehury, Santosh Kumar Behera, Namita Mahapatra
The protein kinases (PKs), belonging to serine/threonine kinase (STKs), are important drug targets for a wide spectrum of diseases in human. Among protein kinases, the Casein Kinases (CKs) are vastly expanded in various organisms, where, the malarial parasite Plasmodium falciparum possesses a single member i.e., PfCKI, which can phosphorylate various proteins in parasite extracts in vitro condition. But, the structure-function relationship of PfCKI and dynamics of ATP binding is yet to be understood. Henceforth, an attempt was made to study the dynamics, stability, and ATP binding mechanisms of PfCKI through computational modelling, docking, molecular dynamics (MD) simulations, and MM/PBSA binding free energy estimation...
November 21, 2016: Journal of Molecular Graphics & Modelling
Christian J Burnham, Zdenek Futera, Niall J English
Building on our previous work (J. Phys. Chem. C, 2016, 120, 16561), using an empirical model we run both classical and path-integral molecular dynamics simulations for a type II clathrate hydrate containing different amounts of guest H2 molecules from 1 to 5 molecules per large cage, with results presented at temperatures of 50, 100 K and 200 K. We present results for the density isosurfaces of the guest molecules at all different occupations and temperatures, showing how the density approaches the perfect tetrahedral structure which has been found for the n = 4 case in which each molecule sits on the vertex of a tetrahedron about the centre of each large cage...
December 6, 2016: Physical Chemistry Chemical Physics: PCCP
Jamal Adiban, Yousef Jamali, Hashem Rafii-Tabar
Activation of voltage-gated calcium channels by action potentials leads to the influx of Ca(2+) ions. In this study, the ion permeation characteristics in bacterial voltage-gated calcium (CaVAb) channels were investigated using molecular dynamics simulations. Furthermore, the potential of mean force (PMF) calculations was evaluated to determine the free energy profile for the permeation of cations (Ca(2+) and Na(+)) and anions (Cl(-)) in the CaVAb channel. The results showed that both Ca(2+) and Na(+) cations experienced a deep energy well, while the Cl(-) anion experienced a relatively high energy barrier at the center of the selectivity filter (site 2)...
December 5, 2016: Molecular BioSystems
Priyanka Tavhare, Amol Deshmukh, Ajay Chaudhari
We have performed an ab initio and density functional theory study of the hydrogen adsorption on a lithium (Li)-decorated pentalene (C8H6Li2) complex. The C8H6Li2 complex can interact with a maximum of two hydrogen molecules with a H2 uptake capacity of 3.36 wt%. The effect of the number and position of boron atom substitution in the C8H6Li2 complex on the H2 uptake capacity is also studied. Two and four carbon atoms are substituted by boron atoms in the C8H6Li2 complex. Two different structures are considered for each of the two and four boron atom substitutions...
December 5, 2016: Physical Chemistry Chemical Physics: PCCP
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"