Effects of Salt on the Lower Critical Solution Temperature of Poly (N-Isopropylacrylamide)
22 Nov 2010-Journal of Physical Chemistry B (American Chemical Society)-Vol. 114, Iss: 49, pp 16594-16604
TL;DR: It is suggested that direct interactions between the salt cations and the polymer play a critical role in the shift of LCST and subsequently on protein stability and the results suggest that cations have a much stronger affinity with the polymer, whereas anions bind weakly withthe polymer.
Abstract: Classical molecular dynamics simulations were performed to investigate the effects of salt on the lower critical solution temperature (LCST) of Poly (N-isopropylacrylamide) (PNIPAM). PNIPAM is often studied as a protein proxy due to the presence of a peptide bond in its monomer unit. PNIPAM is a temperature sensitive polymer which exhibits hydrophobic−hydrophilic phase transition at its LCST. The presence of salt in the solution will shift its LCST, typically to a lower temperature. This LCST shift follows the so-called Hofmeister series. Molecular dynamics (MD) simulations of PNIPAM in 1 M of NaCl, NaBr, NaI, and KCl were carried out to elucidate the effects of different salt on LCST and protein stability. Our results suggest that direct interactions between the salt cations and the polymer play a critical role in the shift of LCST and subsequently on protein stability. Further, cations have a much stronger affinity with the polymer, whereas anions bind weakly with the polymer. Moreover, the cation−polym...
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803 citations
TL;DR: A variety of promising applications, including affinity separation, proteomics, metabolomics, disease diagnostics and aptamer selection, are introduced with main emphasis on how boronate affinity materials can solve the issues in the applications and what merits they can provide.
Abstract: Boronate affinity materials, as unique sorbents, have emerged as important media for the selective separation and molecular recognition of cis-diol-containing compounds. With the introduction of boronic acid functionality, boronate affinity materials exhibit several significant advantages, including broad-spectrum selectivity, reversible covalent binding, pH-controlled capture/release, fast association/desorption kinetics, and good compatibility with mass spectrometry. Because cis-diol-containing biomolecules, including nucleosides, saccharides, glycans, glycoproteins and so on, are the important targets in current research frontiers such as metabolomics, glycomics and proteomics, boronate affinity materials have gained rapid development and found increasing applications in the last decade. In this review, we critically survey recent advances in boronate affinity materials. We focus on fundamental considerations as well as important progress and new boronate affinity materials reported in the last decade. We particularly discuss on the effects of the structure of boronate ligands and supporting materials on the properties of boronate affinity materials, such as binding pH, affinity, selectivity, binding capacity, tolerance for interference and so on. A variety of promising applications, including affinity separation, proteomics, metabolomics, disease diagnostics and aptamer selection, are introduced with main emphasis on how boronate affinity materials can solve the issues in the applications and what merits boronate affinity materials can provide.
400 citations
TL;DR: In this paper, molecular dynamics simulations are used to establish the role of solvation dynamics and local ordering of water in inducing conformational transitions in isotactic-rich poly(N-isopropylacrylamide) (PNIPAM) oligomers when the temperature is changed through the LCST.
Abstract: Conformational transitions in thermo-sensitive polymers are critical in determining their functional properties. The atomistic origin of polymer collapse at the lower critical solution temperature (LCST) remains a fundamental and challenging problem in polymer science. Here, molecular dynamics simulations are used to establish the role of solvation dynamics and local ordering of water in inducing conformational transitions in isotactic-rich poly(N-isopropylacrylamide) (PNIPAM) oligomers when the temperature is changed through the LCST. Simulated atomic trajectories are used to identify stable conformations of the water-molecule network in the vicinity of polymer segments, as a function of the polymer chain length. The dynamics of the conformational evolution of the polymer chain within its surrounding water molecules is evaluated using various structural and dynamical correlation functions. Around the polymer, water forms cage-like structures with hydrogen bonds. Such structures form at temperatures both ...
174 citations
17 Jan 2020
TL;DR: A traditional single drug delivery system cannot achieve desired long-term controlled release of therapeutic drugs in lung cancer patients because of the complex nature of the disease.
Abstract: Lung cancer is a complicated long-term disease, which is extremely difficult to cure. A traditional single drug delivery system cannot achieve desired long-term controlled release of therapeutic co...
171 citations
TL;DR: It was found that molar concentrations of well-hydrated metal cations led to the rise of a peak assigned to metal cation- bound amides and a decrease in the peak associated with purely water-bound amides, which is far weaker than the analogous binding of weakly hydrated anions.
Abstract: We investigated salt interactions with butyramide as a simple mimic of cation interactions with protein backbones. The experiments were performed in aqueous metal chloride solutions using two spectroscopic techniques. In the first, which provided information about contact pair formation, the response of the amide I band to the nature and concentration of salt was monitored in bulk aqueous solutions via attenuated total reflection Fourier transform infrared spectroscopy. It was found that molar concentrations of well-hydrated metal cations (Ca2+, Mg2+, Li+) led to the rise of a peak assigned to metal cation-bound amides (1645 cm–1) and a decrease in the peak associated with purely water-bound amides (1620 cm–1). In a complementary set of experiments, the effect of cation identity and concentration was investigated at the air/butyramide/water interface via vibrational sum frequency spectroscopy. In these studies, metal ion–amide binding led to the ordering of the adjacent water layer. Such experiments were ...
153 citations
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TL;DR: NAMD as discussed by the authors is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems that scales to hundreds of processors on high-end parallel platforms, as well as tens of processors in low-cost commodity clusters, and also runs on individual desktop and laptop computers.
Abstract: NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions, parameters, and file formats. This article, directed to novices as well as experts, first introduces concepts and methods used in the NAMD program, describing the classical molecular dynamics force field, equations of motion, and integration methods along with the efficient electrostatics evaluation algorithms employed and temperature and pressure controls used. Features for steering the simulation across barriers and for calculating both alchemical and conformational free energy differences are presented. The motivations for and a roadmap to the internal design of NAMD, implemented in C++ and based on Charm++ parallel objects, are outlined. The factors affecting the serial and parallel performance of a simulation are discussed. Finally, typical NAMD use is illustrated with representative applications to a small, a medium, and a large biomolecular system, highlighting particular features of NAMD, for example, the Tcl scripting language. The article also provides a list of the key features of NAMD and discusses the benefits of combining NAMD with the molecular graphics/sequence analysis software VMD and the grid computing/collaboratory software BioCoRE. NAMD is distributed free of charge with source code at www.ks.uiuc.edu.
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TL;DR: Weiner et al. as mentioned in this paper derived a new molecular mechanical force field for simulating the structures, conformational energies, and interaction energies of proteins, nucleic acids, and many related organic molecules in condensed phases.
Abstract: We present the derivation of a new molecular mechanical force field for simulating the structures, conformational energies, and interaction energies of proteins, nucleic acids, and many related organic molecules in condensed phases. This effective two-body force field is the successor to the Weiner et al. force field and was developed with some of the same philosophies, such as the use of a simple diagonal potential function and electrostatic potential fit atom centered charges. The need for a 10-12 function for representing hydrogen bonds is no longer necessary due to the improved performance of the new charge model and new van der Waals parameters. These new charges are determined using a 6-31G* basis set and restrained electrostatic potential (RESP) fitting and have been shown to reproduce interaction energies, free energies of solvation, and conformational energies of simple small molecules to a good degree of accuracy. Furthermore, the new RESP charges exhibit less variability as a function of the molecular conformation used in the charge determination. The new van der Waals parameters have been derived from liquid simulations and include hydrogen parameters which take into account the effects of any geminal electronegative atoms. The bonded parameters developed by Weiner et al. were modified as necessary to reproduce experimental vibrational frequencies and structures. Most of the simple dihedral parameters have been retained from Weiner et al., but a complex set of 4 and yj parameters which do a good job of reproducing the energies of the low-energy conformations of glycyl and alanyl dipeptides has been developed for the peptide backbone.
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TL;DR: In this paper, the authors present conformational energies for a molecular mechanical model (Parm99) developed for organic and biological molecules using the restrained electrostatic potential (RESP) approach to derive the partial charges.
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TL;DR: These efforts to build better models of the monovalent ions within the pairwise Coulombic and 6-12 Lennard-Jones framework are described, where the models are tuned to balance crystal and solution properties in Ewald simulations with specific choices of well-known water models.
Abstract: Alkali (Li+, Na+, K+, Rb+, and Cs+) and halide (F−, Cl−, Br−, and I−) ions play an important role in many biological phenomena, roles that range from stabilization of biomolecular structure, to influence on biomolecular dynamics, to key physiological influence on homeostasis and signaling. To properly model ionic interaction and stability in atomistic simulations of biomolecular structure, dynamics, folding, catalysis, and function, an accurate model or representation of the monovalent ions is critically necessary. A good model needs to simultaneously reproduce many properties of ions, including their structure, dynamics, solvation, and moreover both the interactions of these ions with each other in the crystal and in solution and the interactions of ions with other molecules. At present, the best force fields for biomolecules employ a simple additive, nonpolarizable, and pairwise potential for atomic interaction. In this work, we describe our efforts to build better models of the monovalent ions within t...
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