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https://www.readbyqxmd.com/read/30514080/why-computed-protein-folding-landscapes-are-sensitive-to-the-water-model
#1
Ramu Anandakrishnan, Saeed Izadi, Alexey V Onufriev
We investigate the effect of solvent models on the computed thermodynamics of protein folding. Atomistic folding simulations of a fast-folding mini-protein CLN025 were employed to compare two commonly used explicit solvent water models, TIP3P and TIP4P/Ew, and one implicit solvent (AMBER generalized Born) model. Although all three solvent models correctly identify the same native folded state (RMSD = 1.5 ± 0.1 ̊A relative to the experimental structure), the corresponding free energy landscapes vary drastically between water models: almost an order-of-magnitude difference is seen in the predicted fraction of the unfolded state between the two explicit solvent models, with even larger differences between the implicit and the explicit models...
December 4, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/30511014/pamam-dendrimers-as-efficient-drug-and-gene-delivery-nanosystems-for-cancer-therapy
#2
Fereydoon Abedi-Gaballu, Gholamreza Dehghan, Maryam Ghaffari, Reza Yekta, Soheil Abbaspour-Ravasjani, Behzad Baradaran, Jafar Ezzati Nazhad Dolatabadi, Michael R Hamblin
Drug delivery systems for cancer chemotherapy are employed to improve the effectiveness and decrease the side-effects of highly toxic drugs. Most chemotherapy agents have indiscriminate cytotoxicity that affects normal, as well as cancer cells. To overcome these problems, new more efficient nanosystems for drug delivery are increasingly being investigated. Polyamidoamine (PAMAM) dendrimers are an example of a versatile and reproducible type of nanocarrier that can be loaded with drugs, and modified by attaching target-specific ligands that recognize receptors that are over-expressed on cancer cells...
September 2018: Applied Materials Today
https://www.readbyqxmd.com/read/30507985/pyrazole-appended-quinoline-bodipy-based-arene-ruthenium-complexes-their-anticancer-activity-and-potential-applications-in-cellular-imaging
#3
Rajendra Prasad Paitandi, Vinay Sharma, Vishwa Deepak Singh, Bhupendra Kumar Dwivedi, Shaikh M Mobin, Daya Shankar Pandey
Synthesis of an entirely new series of arene ruthenium complexes [Ru(η6-C6H6)(L1)Cl]PF6, (1), [Ru(η6-C10H14)(L1)Cl]PF6 (2), [Ru(η6-C6H6)(L2)Cl]PF6 (3) and [Ru(η6-C10H14)(L2)Cl]PF6 (4) involving 5-[2-(1H-pyrazol-1-yl)quinoline]-BODIPY (L1) and 5-[6-methoxy-2-(1H-pyrazol-1-yl)quinoline]-BODIPY (L2) was described. The ligands and complexes were thoroughly characterized by various physicochemical techniques and the structures of L1, 1 and 4 were determined by X-ray single crystal analyses. Photo-/ and electrochemical property, DNA binding, cytotoxicity, cellular uptake and apoptotic studies on 1-4 were performed by various methods, while singlet oxygen-mediated cytotoxicity via photo-irradiation by visible light was supported by 1,3-diphenylisobenzofuran titration studies...
December 3, 2018: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/30507167/approaching-materials-with-atomic-precision-using-supramolecular-cluster-assemblies
#4
Papri Chakraborty, Abhijit Nag, Amrita Chakraborty, Thalappil Pradeep
Supramolecular chemistry is a major area of chemistry that utilizes weaker non-covalent interactions between molecules, including hydrogen bonding, van der Waals, electrostatic, π···π, and C-H···π interactions. Such forces have been the basis of several molecular self-assemblies and host-guest complexes in organic, inorganic, and biological systems. Atomically precise nanoclusters (NCs) are materials of growing interest that display interesting structure-property correlations. The evolving science of such systems reaffirms their molecular behavior...
December 3, 2018: Accounts of Chemical Research
https://www.readbyqxmd.com/read/30498974/binding-of-histamine-to-the-h1-receptor-a-molecular-dynamics-study
#5
Christian A Söldner, Anselm H C Horn, Heinrich Sticht
Binding of histamine to the G-protein coupled histamine H1 receptor plays an important role in the context of allergic reactions; however, no crystal structure of the resulting complex is available yet. To deduce the histamine binding site, we performed unbiased molecular dynamics (MD) simulations on a microsecond time scale, which allowed to monitor one binding event, in which particularly the residues of the extracellular loop 2 were involved in the initial recognition process. The final histamine binding pose in the orthosteric pocket is characterized by interactions with Asp1073...
November 29, 2018: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/30497059/interaction-of-dequalinium-chloride-with-phosphatidylcholine-bilayers-a-biophysical-study-with-consequences-on-the-development-of-lipid-based-mitochondrial-nanomedicines
#6
Félix Sauvage, François-Xavier Legrand, Michel Roux, Ivan Rajkovic, Thomas M Weiss, Zoltán Varga, Luc Augis, Guillaume Nugue, Jean-Claude Debouzy, Juliette Vergnaud-Gauduchon, Gillian Barratt
Dequalinium (DQ) has been proposed as a mitochondrial targeting ligand for nanomedicines, including liposomes, given the implication of these organelles in many diseases. This original study focuses on the interactions of DQ with phosphatidylcholine bilayers during the formation of liposomes. Firstly, PEGylated liposomes suitable for drug delivery were studied and were found to be more stable when made in water than in phosphate-buffered saline, emphasizing the role of electrostatic interactions between positive charges on DQ and the polar head groups of the lipids...
November 15, 2018: Journal of Colloid and Interface Science
https://www.readbyqxmd.com/read/30488768/interaction-of-anticancer-drug-pinostrobin-with-lysozyme-a-biophysical-and-molecular-docking-approach
#7
Masihuz Zaman, Haaris Ahsan Safdari, Asra Nasir Khan, Syed Mohammad Zakariya, Saima Nusrat, Tajalli Ilm Chandel, Rizwan Hasan Khan
The interaction between drugs and proteins has turned out to be a significant research area in recent years. These interactions offer structural strategy in drug formulations through better medical efficiency. Thus, interaction of a pharmacologically important flavonoid, pinostrobin, with hen egg white lysozyme (HEWL) has been examined using a multitude of spectroscopic techniques including fluorescence spectroscopy, UV-visible spectroscopy, circular dichroism (CD) and dynamic light scattering (DLS) techniques...
November 29, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30481608/cell-armor-for-protection-against-environmental-stress-advances-challenges-and-applications-in-micro-and-nanoencapsulation-of-mammalian-cells
#8
Onur Hasturk, David L Kaplan
Unlike unicellular organisms and plant cells surrounded with a cell wall, naked plasma membranes of mammalian cells make them more susceptible to environmental stresses encountered during in vitro biofabrication and in vivo cell therapy applications. Recent advances in micro- and nanoencapsulation of single mammalian cells provide an effective strategy to isolate cells from their surroundings and protect them against harsh environmental conditions. Microemulsification and droplet-based microfluidics have enabled researchers to encapsulate single cells within a variety of microscale hydrogel materials with a range of biochemical and mechanical properties and functionalities including enhanced cell-matrix interactions or on-demand degradation...
November 24, 2018: Acta Biomaterialia
https://www.readbyqxmd.com/read/30467572/designing-air-stable-cyclometalated-fe-ii-complexes-stabilization-via-electrostatic-effects
#9
Daniel Charles Ashley, Sriparna Mukherjee, Elena Jakubikova
Designing efficient Fe(ii) chromophores requires optimization of numerous, at times conflicting, properties. It has been suggested that replacement of polypyridine ligands with cyclometalated analogs will be effective at destabilizing the quintet state and therefore extending the lifetime of photoactive metal-to-ligand charge transfer states. However, cyclometalated Fe(ii) complexes are not oxidatively stable due to the strong electron-donating nature of this ligand, which limits their applicability. Here we use density functional theory calculations to show how simple addition of nitro and carboxylic acid groups to these cyclometalated complexes can engender a less oxidizable Fe(ii) center while maintaining, or even improving, the favorable ligand field strength...
November 23, 2018: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/30465571/factors-governing-when-a-metal-bound-water-is-deprotonated-in-proteins
#10
Cédric Grauffel, Carmay Lim
Understanding when a metal-bound water molecule in a protein is deprotonated is important as this affects the charge distribution in the metal-binding/enzyme active site and thus their interactions, the enzyme mechanism, and inhibitor design. The protonation state of the metal-bound water molecule at a given pH depends on its pKa value, which in turn depends on the properties of the cation, its ligands, and the protein environment. Here, we reveal how and the extent to which (i) the first-shell composition (type, charge, and number of ligands), (ii) the metal site's immediate surroundings (first-shellsecond-shell hydrogen-bonding interactions, metal-ligand distance constraints, and ligand-binding mode) and (iii) the protein architecture and coupled solvent interactions (long-range electrostatic interactions and solvent exposure of the site) affect the Zn2+-bound water pKa...
November 22, 2018: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/30454702/rational-affinity-enhancement-of-fragmented-antibody-by-ligand-based-affinity-improvement-approach
#11
Zahra Ebrahimi, Saeme Asgari, Reza Ahangari Cohan, Reza Hosseinzadeh, Ghader Hosseinzadeh, Roghaye Arezumand
Antibody engineering is now a noteworthy area in biopharmaceuticals as the next generation of marketed antibodies is engineered antibodies such as affinity- or stability-improved antibodies, fragmented or fused antibodies, antibody drug conjugates (ADCs), and PEGylated antibody fragments. In the current study, affinity enhancement of Nb against PlGF was performed by an in silico affinity maturation and molecular dynamics (MD) simulation. First, 300 single-point mutants were designed by identifying the residues involved in interaction with PlGF and different energy distributions...
November 30, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/30444912/probing-inhibition-mechanisms-of-adenosine-deaminase-by-using-molecular-dynamics-simulations
#12
Xiaopian Tian, Ye Liu, Jingxuan Zhu, Zhengfei Yu, Jiarui Han, Yan Wang, Weiwei Han
Adenosine deaminase (ADA) catalyzes the deamination of adenosine, which is important in purine metabolism. ADA is ubiquitous to almost all human tissues, and ADA abnormalities have been reported in various diseases, including rheumatoid arthritis. ADA can be divided into two conformations based on the inhibitor that it binds to: open and closed forms. Here, we chose three ligands, namely, FR117016 (FR0), FR221647 (FR2) (open form), and HDPR (PRH, closed form), to investigate the inhibition mechanism of ADA and its effect on ADA through molecular dynamics simulations...
2018: PloS One
https://www.readbyqxmd.com/read/30428307/modular-core-shell-polymeric-nanoparticles-mimicking-viral-structures-for-vaccination
#13
Bo Lou, Ans De Beuckelaer, Eger Boonstra, Dandan Li, Bruno G De Geest, Stefaan De Koker, Enrico Mastrobattista, Wim E Hennink
Recent advances in the development of protein-based vaccines have expanded the opportunities for preventing and treating both infectious diseases as well as cancer. However, the development of readily and efficient antigen delivery systems capable of stimulating strong cytotoxic T-lymphocyte (CTL) responses remains a challenge. With the attempt to closely mimic the properties of viruses in terms of their size and molecular organization, we constructed RNA (which is a ligand for Toll-like receptor 7 (TLR7) and TLR8) and antigen-loaded nanoparticles resembling the structural organization of viruses...
November 11, 2018: Journal of Controlled Release: Official Journal of the Controlled Release Society
https://www.readbyqxmd.com/read/30427801/efficient-capture-of-phosphate-from-aqueous-solution-using-acid-activated-akadama-clay-and-mechanisms-analysis
#14
Ying Wang, Hui He, Nan Zhang, Kazuya Shimizu, Zhongfang Lei, Zhenya Zhang
In this study, akadama clay, a kind of volcano ash, was activated with sulfuric acid and then evaluated for the adsorption of phosphate from aqueous solution via batch experiments. The effects of adsorbent dose, initial pH and coexisting anions on phosphate removal by natural akadama clay and acid-activated akadama clay were investigated. Based on the pH effect, the modified adsorbent could efficiently capture phosphate over a wider pH range of 3.00-6.00 than natural akadama clay. Competitive anions showed negative effects on the phosphate adsorption, especially citrate and carbonate...
November 2018: Water Science and Technology: a Journal of the International Association on Water Pollution Research
https://www.readbyqxmd.com/read/30423939/molecular-modeling-and-design-studies-of-purine-derivatives-as-novel-cdk2-inhibitors
#15
Gaomin Zhang, Yujie Ren
Cyclin-dependent kinase 2 (CDK2) is a potential target for treating cancer. Purine heterocycles have attracted particular attention as the scaffolds for the development of CDK2 inhibitors. To explore the interaction mechanism and the structure⁻activity relationship (SAR) and to design novel candidate compounds as potential CDK2 inhibitors, a systematic molecular modeling study was conducted on 35 purine derivatives as CDK2 inhibitors by combining three-dimensional quantitative SAR (3D-QSAR), virtual screening, molecular docking, and molecular dynamics (MD) simulations...
November 9, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/30418582/tethered-imidazole-mediated-duplex-stabilization-and-its-potential-for-aptamer-stabilization
#16
Lars Verdonck, Dieter Buyst, Anne-Mare de Vries, Vicky Gheerardijn, Annemieke Madder, José C Martins
Previous investigations of the impact of an imidazole-tethered thymidine in synthetic DNA duplexes, monitored using UV and NMR spectroscopy, revealed a base context dependent increase in thermal stability of these duplexes and a striking correlation with the imidazolium pKa. Unrestrained molecular dynamics (MD) simulations demonstrated the existence of a hydrogen bond between the imidazolium and the Hoogsteen side of a nearby guanosine which, together with electrostatic interactions, form the basis of the so-called pKa-motif responsible for these duplex-stabilizing and pKa-modulating properties...
November 10, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/30417659/design-identification-antifungal-evaluation-and-molecular-modeling-of-chlorotetaine-derivatives-as-new-anti-fungal-agents
#17
Xiao Huan Liu, Jiong Feng Zhao, Tao Wang, Mian Bin Wu
It is feasible to rationally modify existing bioactive components for new drug development, achieving molecules with improved biological activities. In this study, rational modification of chlorotetaine was carried out following in silico molecular modelling to enhance interactions between the fungal oligopeptide transmembrane transporter PTR22 and the ligand. The peptide obtained with the lowest docking energy, Lys-chlorotetaine (LC), displayed an improved antifungal effect compared with chlorotetaine. The lowest minimum inhibitory concentration observed against a tested pathogen was 1...
November 10, 2018: Natural Product Research
https://www.readbyqxmd.com/read/30416518/structural-properties-and-reactive-site-selectivity-of-some-transition-metal-complexes-of-2-2-1e-1-e-ethane-1-2-diylbis-azan-1-yl-1-ylidene-bis-phenylmethan-1-yl-1-ylidene-dibenzoic-acid-dft-conceptual-dft-qtaim-and-mep-studies
#18
Fritzgerald Kogge Bine, Nyiang Kennet Nkungli, Tasheh Stanley Numbonui, Julius Numbonui Ghogomu
Herein is presented a density functional theory (DFT) study of reactivity and structural properties of transition metal complexes of the Schiff base ligand 2,2'(1E,1'E)-(ethane-1,2-diylbis(azan-1-yl-1-ylidene))bis(phenylmethan-1-yl-1-ylidene)dibenzoic acid (hereafter denoted EDA2BB) with Cu(II), Mn(II), Ni(II), and Co(II). The quantum theory of atoms-in-molecules (QTAIM), conceptual DFT, natural population analysis (NPA), and molecular electrostatic potential (MEP) methods have been used. Results have revealed a distorted octahedral geometry around the central metal ion in each gas phase complex...
2018: Bioinorganic Chemistry and Applications
https://www.readbyqxmd.com/read/30408966/switching-of-binding-site-from-nonpolar-to-polar-ligands-toward-cationic-benzonitrile-revealed-by-infrared-spectroscopy
#19
Kuntal Chatterjee, Otto Dopfer
Noncovalent interactions of aromatic molecules in their various charge states with their surrounding environment are of fundamental importance in chemistry and biology. Herein, we analyze the infrared photodissociation spectra of mass-selected cationic clusters of benzonitrile (BN, cyanobenzene, C6 H5 CN) with L = Ar, N2 , and H2 O (W), in the CH and OH stretch range (2950-3800 cm-1 ) with the aid of density functional theory calculations at the dispersion-corrected B3LYP-D3/aug-cc-pVTZ level to probe the interaction of this fundamental aromatic cation in its 2 B1 ground electronic state with nonpolar, quadrupolar, and dipolar solvent molecules...
November 7, 2018: Journal of Chemical Physics
https://www.readbyqxmd.com/read/30404956/revisiting-the-interaction-force-measurement-between-lipid-bilayers-using-a-surface-forces-apparatus-sfa
#20
Dong Woog Lee
In this review, previous researches that measured intermembrane forces using the Surface Forces Apparatus are recapitulated. Different types of interaction forces are reported between two lipid bilayers including non-specific interactions (e.g., van der Waals, electrostatic, steric hydration, thermal undulation, and hydrophobic) and specific interactions (e.g., ligand-receptor). By measuring absolute distance and interaction forces at the sub-angstrom level and at a few nano-Newtons resolution, respectively, magnitudes, working ranges, and decay lengths of interaction between lipid bilayers are investigated...
2018: Journal of Oleo Science
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