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biomolecular interaction

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
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 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
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
Sibaprasad Maity, Ekaterina Viazovkina, Alexander Gall, Yuri Lyubchenko
Probing of biomolecular complexes by single-molecule force spectroscopy (SMFS) methods including AFM requires proper and suitable coupling methods for immobilization of biomolecules onto the AFM tip and the surface. The use of flexible tethers for the coupling process has dual advantages. First, they allow the specific immobilization of interacting molecules, and second, their flexibility facilitates the proper orientation of the interacting partners. Recently, we developed an approach termed Flexible Nano Array (FNA) in which interacting partners are located on the same polymeric FNA molecule separated by a flexible segment with a defined length...
2016: Journal of Nature and Science
Pritha Ghosh, Oommen K Mathew, Ramanathan Sowdhamini
BACKGROUND: RNA-binding proteins (RBPs) interact with their cognate RNA(s) to form large biomolecular assemblies. They are versatile in their functionality and are involved in a myriad of processes inside the cell. RBPs with similar structural features and common biological functions are grouped together into families and superfamilies. It will be useful to obtain an early understanding and association of RNA-binding property of sequences of gene products. Here, we report a web server, RStrucFam, to predict the structure, type of cognate RNA(s) and function(s) of proteins, where possible, from mere sequence information...
October 7, 2016: BMC Bioinformatics
Hui Wang, Ke Ma, Bin Xu, Wenjing Tian
Aggregation-induced emission (AIE) probes have shown great potential applications in fluorescent sensing of biomolecules, and the integration of AIE probe and graphene oxide (GO) attracts intense interest in developing new tools for label-free and "turn-on" fluorescent biomolecular analysis. Herein, an ultrasensitive label-free and "turn-on" DNA sensing is realized by tuning the supramolecular interactions of AIE probe and GO with DNA. The investigation of supramolecular interactions of AIE probes and GO with DNA demonstrate that AIE probe with short alkyl chains substitute shows highest binding affinity with DNA strand, and GO with low oxidation degree possesses strong binding interactions to ssDNA and the highest fluorescence quenching efficiency...
September 26, 2016: Small
Shu-Cheng Lo, En-Hung Lin, Pei-Kuen Wei, Wan-Shao Tsai
In this study, we demonstrate a compact imaging spectroscopic system for high-throughput detection of biomolecular interactions on plasmonic chips, based on a curved grating as the key element of light diffraction and light focusing. Both the curved grating and the plasmonic chips are fabricated on flexible plastic substrates using a gas-assisted thermal-embossing method. A fiber-coupled broadband light source and a camera are included in the system. Spectral resolution within 1 nm is achieved in sensing environmental index solutions and protein bindings...
October 17, 2016: Analyst
Yujie Zhu, Jose M Moran-Mirabal
Supported lipid bilayers (SLBs) provide an excellent model system for studying structural and functional characteristics of biomembranes. Patterning model membranes on solid supports has elicited much interest because lipid bilayer arrays at cellular or sub-cellular scales provide attractive platforms for reconstituting tissue-like conditions for cell culture, and for creating simplified physiological environments to study biological processes. Phase-segregated SLB patterns can be especially useful for such studies, as the selective functionalization of the lipid phases with different lipids, receptors or proteins can be achieved to mimic the key features of plasma membrane...
October 4, 2016: Langmuir: the ACS Journal of Surfaces and Colloids
Guo-Hua Jin, Wei Xu, Yang Shi, Li-Bo Wang
Gastric cancer (GC) is a prevalent cancer, which remains incurable, and therefore requires an alternative treatment method. Celecoxib is a nonsteroidal anti-inflammatory drug that targets cyclooxygenase-2, and exhibits anticancer effects. The present study aimed to investigate the anti-GC mechanism of celecoxib using bioinformatics methods. Gene expression datasets GSE56807 (GC tissues and normal gastric tissues) and GSE54657 (celecoxib-treated and non-treated human GC epithelial AGS cells) were downloaded from the Gene Expression Omnibus database...
October 2016: Oncology Letters
Francesco Raimondi, Gurdeep Singh, Matthew J Betts, Gordana Apic, Ranka Vukotic, Pietro Andreone, Lincoln Stein, Robert B Russell
To attain a deeper understanding of diseases like cancer, it is critical to couple genetics with biomolecular mechanisms. High-throughput sequencing has identified thousands of somatic mutations across dozens of cancers, and there is a pressing need to identify the few that are pathologically relevant. Here we use protein structure and interaction data to interrogate nonsynonymous somatic cancer mutations, identifying a set of 213 molecular interfaces (protein-protein, -small molecule or -nucleic acid) most often perturbed in cancer, highlighting several potentially novel cancer genes...
October 4, 2016: Scientific Reports
Shu Hui Hiew, Paul A Guerette, Ondrej J Zvarec, Margaret Phillips, Feng Zhou, Haibin Su, Konstantin Pervushin, Brendan P Orner, Ali Miserez
: The hard sucker ring teeth (SRT) from decapodiforme cephalopods, which are located inside the sucker cups lining the arms and tentacles of these species, have recently emerged as a unique model structure for biomimetic structural biopolymers. SRT are entirely composed of modular, block co-polymer-like proteins that self-assemble into a large supramolecular network. In order to unveil the molecular principles behind SRT's self-assembly and robustness, we describe a combinatorial screening assay that maps the molecular-scale interactions between the most abundant modular peptide blocks of suckerin proteins...
September 29, 2016: Acta Biomaterialia
Hanif M Khan, Cédric Grauffel, Ria Broer, Alexander D MacKerell, Remco W A Havenith, Nathalie Reuter
Cation-π interactions between tyrosine amino acids and compounds containing N,N,N-trimethylethanolammonium (N(CH3)3) are involved in the recognition of histone tails by chromodomains and in the recognition of phosphatidylcholine (PC) phospholipids by membrane-binding proteins. Yet, the lack of explicit polarization or charge transfer effects in molecular mechanics force fields raises questions about the reliability of the representation of these interactions in biomolecular simulations. Here, we investigate the nature of phenol-tetramethylammonium (TMA) interactions using quantum mechanical (QM) calculations, which we also use to evaluate the accuracy of the additive CHARMM36 and Drude polarizable force fields in modeling tyrosine-choline interactions...
October 13, 2016: Journal of Chemical Theory and Computation
Konstantin G Shevchenko, Vladimir R Cherkasov, Andrey A Tregubov, Petr I Nikitin, Maxim P Nikitin
Biomolecule-driven assembly of nanoparticles is a powerful and convenient approach for development of advanced nanosensors and theranostic agents with diverse "on-demand" composition and functionality. While a lot of research is being devoted to fabrication of such agents, the development of non-invasive analytical tools to monitor self-assembly/disassembly processes in real-time substantially lags behind. Here, we demonstrate the capabilities of localized surface plasmon resonance (SPR) phenomenon to study non-covalent interactions not just between plasmonic particles, but between gold nanoparticles (AuNP) and non-plasmonic ones...
September 12, 2016: Biosensors & Bioelectronics
Thomas H Sharp, Frank G A Faas, Abraham J Koster, Piet Gros
Phase plates in cryo-electron tomography (cryoET) improve contrast, increasing the ability to discern separate molecules and molecular complexes in dense biomolecular environments. Here, we applied this new technology to the activation of the human complement system. Binding of C1 to antigen-antibody complexes initiates a cascade of proteolytic events that deposits molecules onto adjacent surfaces and terminates with the formation of membrane-attack-complex (MAC) pores in the targeted membranes. We imaged steps in this process using a Volta phase plate mounted on a Titan Krios equipped with a Falcon-II direct electron detector...
September 20, 2016: Journal of Structural Biology
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