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Hao Zhu, Jiangli Fan, Huiying Mu, Tao Zhu, Zhen Zhang, Jianjun Du, Xiaojun Peng
Polarity-sensitive fluorescent probes are powerful chemical tools for studying biomolecular structures and activities both in vitro and in vivo. However, the lack of "off-on" polarity-sensing probes has limited the accurate monitoring of biological processes that involve an increase in local hydrophilicity. Here, we design and synthesize a series of "off-on" polarity-sensitive fluorescent probes BP series consisting of the difluoroboron dippyomethene (BODIPY) fluorophore connected to a quaternary ammonium moiety via different carbon linkers...
October 21, 2016: Scientific Reports
Hahnbeom Park, Philip Bradley, Per Greisen, Yuan Liu, Vikram Khipple Mulligan, David E Kim, David Baker, Frank DiMaio
Most biomolecular modeling energy functions for structure prediction, sequence design, and molecular docking, have been parameterized using existing macromolecular structural data; this contrasts molecular mechanics force fields which are largely optimized using small-molecule data. In this study, we describe an integrated method that enables optimization of a biomolecular modeling energy function simultaneously against small-molecule thermodynamic data and high-resolution macromolecular structural data. We use this approach to develop a next-generation Rosetta energy function that utilizes a new anisotropic implicit solvation model, and an improved electrostatics and Lennard-Jones model, illustrating how energy functions can be considerably improved in their ability to describe large-scale energy landscapes by incorporating both small-molecule and macromolecule data...
October 21, 2016: Journal of Chemical Theory and Computation
Michel Alain Cuendet, Harel Weinstein, Michael V LeVine
Allostery plays a fundamental role in most biological processes. However, little theory is available to describe it outside of two-state models. Here we use a statistical mechanical approach to show that the allosteric coupling between two collective variables is not a single number, but instead a two-dimensional thermodynamic coupling function that is directly related to the mutual information from information theory and the copula density function from probability theory. On this basis, we demonstrate how to quantify the contribution of specific energy terms to this thermodynamic coupling function, enabling an approximate decomposition that reveals the mechanism of allostery...
October 21, 2016: Journal of Chemical Theory and Computation
Peter J Gawthrop, Edmund J Crampin
Bond graphs can be used to build thermodynamically-compliant hierarchical models of biomolecular systems. As bond graphs have been widely used to model, analyse and synthesise engineering systems, this study suggests that they can play the same rôle in the modelling, analysis and synthesis of biomolecular systems. The particular structure of bond graphs arising from biomolecular systems is established and used to elucidate the relation between thermodynamically closed and open systems. Block diagram representations of the dynamics implied by these bond graphs are used to reveal implicit feedback structures and are linearised to allow the application of control-theoretical methods...
October 2016: IET Systems Biology
Jun Hyuk Heo, Gyu Sung Yi, Byoung Sang Lee, Hui Hun Cho, Jin Woong Lee, Jung Heon Lee
Here, we report the development of an achromatic nanoparticle-based colorimetric sensor (achromatic nanosensor) with an on-off type color change that significantly enhances the color transition and increases the sensitivity of the sensor for naked-eye inspection. The achromatic nanosensor was prepared via a modified CMYK (CRYK) subtractive color model by combining DNA-functionalized gold nanoparticles (AuNPs-DNA), silver nanoparticles (AgNPs-DNA), and gold nanorods (AuNRs-DNA). The initially black-colored achromatic nanosensor not only allowed multiplexed detection by generating target-specific diverse color changes, but also improved the recognition of color changes by the naked eye...
October 20, 2016: Nanoscale
Noor Asidah Mohamed, Richard T Bradshaw, Jonathan W Essex
The effects of electronic polarization in biomolecular interactions will differ depending on the local dielectric constant of the environment, such as in solvent, DNA, proteins, and membranes. Here the performance of the AMOEBA polarizable force field is evaluated under nonaqueous conditions by calculating the solvation free energies of small molecules in four common organic solvents. Results are compared with experimental data and equivalent simulations performed with the GAFF pairwise-additive force field...
October 19, 2016: Journal of Computational Chemistry
John E Stone, William R Sherman, Klaus Schulten
Immersive molecular visualization provides the viewer with intuitive perception of complex structures and spatial relationships that are of critical interest to structural biologists. The recent availability of commodity head mounted displays (HMDs) provides a compelling opportunity for widespread adoption of immersive visualization by molecular scientists, but HMDs pose additional challenges due to the need for low-latency, high-frame-rate rendering. State-of-the-art molecular dynamics simulations produce terabytes of data that can be impractical to transfer from remote supercomputers, necessitating routine use of remote visualization...
May 2016: IEEE International Symposium on Parallel & Distributed Processing, Workshops and Phd Forum: [proceedings]
Frances J Harding, Salvatore Surdo, Bahman Delalat, Chiara Cozzi, Roey Elnathan, Stan Gronthos, Nicolas H Voelcker, Giuseppe Barillaro
Ordered arrays of silicon nano- to microscale pillars are used to enable biomolecular trafficking into primary human cells, consistently demonstrating high transfection efficiency can be achieved with broader and taller pillars that reported to date. Cell morphology on the pillar arrays is often strikingly elongated. Investigation of the cellular interaction with the pillar reveals that cells are suspended on pillar tips and do not interact with the substrate between the pillars. While cells remain suspended on pillar tips, acute local deformation of the cell membrane was noted, allowing pillar tips to penetrate the cell interior, while retaining cell viability...
October 17, 2016: ACS Applied Materials & Interfaces
Sukhithasri Vijayrajratnam, Anju Choorakottayil Pushkaran, Aathira Balakrishnan, Anilkumar Vasudevan, Raja Gopi Biswas, Chethampadi Gopi Mohan
Nucleotide-binding oligomerization domain-containing protein 1 (NOD1) is an intracellular pattern recognition receptor that recognizes bacterial peptidoglycan (PG) containing meso -diaminopimelic acid ( meso DAP) and activates the innate immune system. Interestingly, few pathogenic and commensal bacteria modify their PG stem peptide by amidation of meso DAP ( meso DAPNH2). In this study, NOD1 stimulation assays were performed using bacterial PG containing meso DAP (PGDAP) and meso DAPNH2 (PGDAPNH2) to understand the differences in their biomolecular recognition mechanism...
October 14, 2016: Biochemical Journal
Francesca T Cannizzo, Sara Pegolo, Paola Pregel, Elisabetta Manuali, Sonia Salamida, Sara Divari, Frine E Scaglione, Enrico Bollo, Bartolomeo Biolatti, Luca Bargelloni
In livestock production corticosteroids are licensed only for therapy, nevertheless they are often illegally used as growth promoters. The aim of this study was to identify morphological or biomolecular alterations induced by prednisolone (PDN) in experimentally treated beef cattle, since PDN and its metabolites are no longer detectable by LC-MS/MS methods in biological fluids. Moreover, PDN do not induce any histological alterations in thymus, differently from Dexamethasone treatments. Therefore, a marker of illicit treatment for this growth promoter could be useful...
October 14, 2016: Journal of Agricultural and Food Chemistry
Aidan I Brown, David A Sivak
At molecular scales, fluctuations play a significant role and prevent biomolecular processes from always proceeding in a preferred direction, raising the question of how limited amounts of free energy can be dissipated to obtain directed progress. We examine the system and process characteristics that efficiently break time-reversal symmetry at fixed energy loss; in particular for a simple model of a molecular machine, an intermediate energy barrier produces unusually high asymmetry for a given dissipation...
September 2016: Physical Review. E
Vitaly K Koltover
There are two generally known concepts in biology of aging. Accordingly to the first one, there is a program of aging. The alternative concept advocates that aging proceeds stochastically. In this area of research, free radical-theory of aging, which was put forward by Denham Harman in fifties of XXth century, has determined the most heuristic line. The goal of this review is to demonstrate how the aging program and the aging stochastics are united on the basis of the systems theory of reliability. On this basis, universal features of aging, such as the exponential growth of mortality rate with time and correlation of longevity with the species-specific resting metabolism, are naturally explained...
October 9, 2016: Current Aging Science
Wei-Wei Zhao, Xiao-Dong Yu, Jing-Juan Xu, Hong-Yuan Chen
Photoelectrochemical (PEC) bioanalysis is a newly developed technique for innovative biomolecular detection. Quantum dots (QDs) with unique photophysical properties are key components in realization of various exquisite PEC bioanalyses. Particularly, significant progress has been made in the QD-based PEC bioanalysis. In this work, we briefly summarize the most recent and important developments in the use of traditional and newly emerging QDs for novel PEC bioanalytical applications. The future prospects in this dynamic field are also highlighted...
October 14, 2016: Nanoscale
Melina K Robinson, Jacob I Monroe, M Scott Shell
Implicit solvation models have long been sought as routes to significantly increase the speed and capabilities of biomolecular simulations. However, it has not always been clear that force fields developed independently of solvation models can together accurately predict secondary structure and folding, and whether the separate influences of the solvation and force field models can be described as independent and additive (versus synergistic). Here, we test two implicit solvation models with several recently-developed protein force fields, within the AMBER simulation package...
October 12, 2016: Journal of Chemical Theory and Computation
M C Bacchus-Montabonel, F Calvo
Solvation effects are of major interest in the context of radiation damage, due to their potential applications in cancer therapy. Reliable modeling of the solvent is, however, quite challenging, and numerous studies have been devoted to isolated biomolecules and stepwise-hydrated molecules in which the amount of solvent is controlled one molecule at a time. The influence of stepwise hydration on radiation damage is investigated here using the example of proton-induced charge transfer in two biomolecular targets...
November 2016: Journal of Molecular Modeling
Celine A Mandon, Loïc Jacques Blum, Christophe Andre Marquette
3D printing technologies will impact in a near future the biosensor community, both at the sensor prototyping level and the sensing layer or-ganization level. The present study aimed at demonstrating the capacity of one 3D printing technique, the Digital Light Processing (DLP), to produce hydrogel sensing layers with 3D shapes unreachable using conventional molding procedures. The first model of sensing layer was com-posed of a sequential enzymatic reaction (glucose oxidase and peroxidase) which generated chemiluminescent signal in the presence of glucose and luminol...
October 11, 2016: Analytical Chemistry
Lara Massai, Alessandro Pratesi, Jovana Bogojeski, Marco Banchini, Serena Pillozzi, Luigi Messori, Živadin D Bugarčić
Three Pd(II) and Pt(II) complexes with chelating mono(imidazolin-2-imine) and bis(imidazolin-2-imine) ligands i.e. [Pd(DMEAIm(iPr))Cl2] (1) (DMEAIm(iPr), 2-(1,3-diisopropyl-4,5-dimethylimidazolin-2-imine)ethan-1-dimethylamine), [Pd(DACH(Im(iPr))2)Cl2] (2) (DACH(Im(iPr))2, N,N'-(cyclohexane-1,2-diyl)bis(1,3-diisopropyl-4,5-dimethylimidazolin-2-imine)) and [Pt(DMEAIm(iPr))Cl2] (3), are evaluated here as potential cytotoxic and anticancer agents. An acceptable solution behaviour was found for the three study compounds in terms of solubility and stability...
September 30, 2016: Journal of Inorganic Biochemistry
Aravind Chandrasekaran, Justin Chan, Carmay Lim, Lee-Wei Yang
Structure-encoded conformational dynamics are crucial for biomolecular functions. However, there is insufficient evidence to support the notion that dynamics plays a role in guiding protein-nucleic acid interactions. Here, we show that protein-DNA docking orientation is a function of protein intrinsic dynamics but the binding site itself does not display unique patterns in the examined spectrum of motions. This revelation is made possible by a novel technique that locates 'dynamics interfaces' in proteins across which protein parts are anti-correlated in their slowest dynamics...
October 10, 2016: Journal of Chemical Theory and Computation
Juyeong Kim, Matthew R Jones, Zihao Ou, Qian Chen
We use liquid phase transmission electron microscopy (LP-TEM) to characterize the structure and dynamics of a solution-phase superlattice assembled from gold nanoprisms at the single particle level. The lamellar structure of the superlattice, determined by a balance of inter-prism interactions, is maintained and resolved under low-dose imaging conditions typically reserved for biomolecular imaging. In this dose range, we capture dynamic structural changes in the superlattice in real time, where contraction and smaller steady-state lattice constants are observed at higher electron dose rates...
October 10, 2016: ACS Nano
Arnfinn Hykkerud Steindal, Maarten T P Beerepoot, Magnus Ringholm, Nanna Holmgaard List, Kenneth Ruud, Jacob Kongsted, Jógvan Magnus Haugaard Olsen
We present the theory and implementation of an open-ended framework for electric response properties at the level of Hartree-Fock and Kohn-Sham density functional theory that includes effects from the molecular environment modeled by the polarizable embedding (PE) model. With this new state-of-the-art multiscale functionality, electric response properties to any order can be calculated for molecules embedded in polarizable atomistic molecular environments ranging from solvents to complex heterogeneous macromolecules such as proteins...
October 12, 2016: Physical Chemistry Chemical Physics: PCCP
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