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biomolecular interaction

Yu Tian, Huixi Violet Zhang, Kristi L Kiick, Jeffery G Saven, Darrin J Pochan
Natural biomolecular self-assembly typically occurs under a narrow range of solution conditions, and the design of sequences that can form prescribed structures under a range of such conditions would be valuable in the bottom-up assembly of predetermined nanostructures. We present a computationally designed peptide that robustly self-assembles into regular arrays under a wide range of solution pH and temperature conditions. Controling the solution conditions provides the opportunity to exploit a simple and reproducible approach for altering the pathway of peptide solution self-assembly...
June 22, 2017: Organic & Biomolecular Chemistry
Marina Tanasova, Joseph R Fedie
Facilitative carbohydrate transporters - Gluts - have received a wide attention over decades due to their essential role in the nutrient uptake and links with various metabolic disorders, including diabetes, obesity, and cancer. Endeavors into understanding mechanisms of Glut-mediated nutrient uptake have resulted in the multidisciplinary research field, branching protein chemistry, chemical biology, organic synthesis, crystallography, and biomolecular modeling. Gluts became attractive targets for cancer research and medicinal chemistry, leading to the development of new approaches to cancer diagnostics and providing avenues for cancer-targeting therapeutics...
June 21, 2017: Chembiochem: a European Journal of Chemical Biology
Maria Kokkinopoulou, Johanna Simon, Katharina Landfester, Volker Mailänder, Ingo Lieberwirth
The use of nanocarriers in biology and medicine is complicated by the current need to understand how nanoparticles interact in complex biological surroundings. When nanocarriers come into contact with serum, proteins immediately adsorb onto their surface, forming a protein corona which defines their biological identity. Although the composition of the protein corona has been widely determined by proteomics, its morphology still remains unclear. In this study we show for the first time the morphology of the protein corona using transmission electron microscopy...
June 20, 2017: Nanoscale
Bita Malekian, Kunli Xiong, Gustav Emilsson, Jenny Andersson, Cecilia Fager, Eva Olsson, Elin M Larsson-Langhammer, Andreas B Dahlin
Plasmonic nanostructures are widely used for various sensing applications by monitoring changes in refractive index through optical spectroscopy or as substrates for surface enhanced Raman spectroscopy. However, in most practical situations conventional surface plasmon resonance is preferred for biomolecular interaction analysis because of its high resolution in surface coverage and the simple single-material planar interface. Still, plasmonic nanostructures may find unique sensing applications, for instance when the nanoscale geometry itself is of interest...
June 20, 2017: Sensors
Kritee Pant, Johanna Pufe, Kristof Zarschler, Ralf Bergmann, Jörg Steinbach, Sabine Reimann, Rainer Haag, Jens Pietzsch, Holger Stephan
Dendritic polyglycerols (dPG) are water soluble, polyether-based nanomaterials which hold great potential in diagnostic as well as therapeutic applications. In order to translate them for in vivo applications, a systematic assessment regarding their cell and tissue interactions as well as their metabolic fate in vivo is a crucial step. Herein, we explore the structure-activity relationship of three different sizes (ca. 3, 5, and 10 nm) of neutral dendritic polyglycerol (dPG) and their corresponding negatively charged sulfate analogs (dPGS) on their in vitro and in vivo characteristics...
June 15, 2017: Nanoscale
Clarisse Gravina Ricci, Bo Li, Li-Tien Cheng, Joachim Dzubiella, J Andrew McCammon
Solvation is a fundamental driving force in many biological processes including biomolecular recognition and self-assembly, not to mention protein folding, dynamics, and function. The Variational Implicit Solvent Method (VISM) is a theoretical tool currently developed and optimized to estimate solvation free energies for systems of very complex topology, such as biomolecules. VISM's theoretical framework makes it unique because it couples hydrophobic, van der Waals and electrostatic interactions as a functional of the solvation interface...
June 14, 2017: Journal of Physical Chemistry. B
Veysel T Yilmaz, Ceyda Icsel, Jenaidullah Batur, Seyma Aydinlik, Murat Cengiz, Orhan Buyukgungor
A series of new silver(i) 5,5-diethylbarbiturate (barb) complexes with the formulas [Ag2(μ-barb)2(PPh3)2] (1), [Ag(barb)(PPh2Cy)] (2), [Ag(barb)(PPhCy2)] (3) and [Ag(barb)(PCy3)] (4) (PPh3 = triphenylphosphine, PPh2Cy = diphenylcyclohexylphosphine, PPhCy2 = dicyclohexylphenylphosphine and PCy3 = tricyclohexylphosphine) were synthesized and fully characterized by elemental analysis, IR, NMR, ESI-MS and X-ray crystallography. All the complexes display a significant affinity towards DNA with a groove binding mode and also strongly bind to BSA via hydrophobic interactions...
June 13, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
Shahar Sukenik, Pin Ren, Martin Gruebele
Weakly bound protein complexes play a crucial role in metabolic, regulatory, and signaling pathways, due in part to the high tunability of their bound and unbound populations. This tunability makes weak binding (micromolar to millimolar dissociation constants) difficult to quantify under biologically relevant conditions. Here, we use rapid perturbation of cell volume to modulate the concentration of weakly bound protein complexes, allowing us to detect their dissociation constant and stoichiometry directly inside the cell...
June 12, 2017: Proceedings of the National Academy of Sciences of the United States of America
Wei Xiao, Zenghui He, Meijian Sun, Shiliang Li, Honglin Li
Water molecules play a crucial role in biomolecular associations by mediating a hydrogen bond network or filling spaces with van der Waals interactions. Although current drug design technologies have taken water molecule interactions into account, their applications are still limited to their reliance on either excessive computer resources or a particular potential energy model. Here, we introduce a statistical method that is based on experimentally-determined water molecules in the binding sites of high-resolution X-ray crystal structures to predict the potential hydration sites in the binding sites of a crystal structures of interest...
June 12, 2017: Journal of Chemical Information and Modeling
Sebastián A Díaz, Soumyo Sen, Kelly Boeneman Gemmill, Carl W Brown, Eunkeu Oh, Kimihiro Susumu, Michael H Stewart, Joyce C Breger, Guillermo Lasarte Aragonés, Lauren D Field, Jeffrey R Deschamps, Petr Král, Igor L Medintz
Combining biomolecules such as enzymes with nanoparticles has much to offer for creating next generation synergistically functional bionanomaterials. However, almost nothing is known about how these two disparate components interact at this critical biomolecular-materials interface to give rise to improved activity and emergent properties. Here we examine how the nanoparticle surface can influence and increase localized enzyme activity using a designer experimental system consisting of trypsin proteolysis acting on peptide-substrates displayed around semiconductor quantum dots (QDs)...
June 12, 2017: ACS Nano
Muslim Raza, Yang Jiang, Yun Wei, Aftab Ahmad, Ajmal Khan, Yuan Qipeng
The study of molecular interactions of drug-protein are extremely important from the biological aspect in all living organisms, and therefore such type of investigation hold a tremendous significance in rational drug design and discovery. In the present study, the molecular interactions between paromomycin (PAR) and human serum albumin (HSA) have been studied by different biophysical techniques and validated by in-silico approaches. The results obtained from Ultraviolet-visible spectroscopy (UV) and Fourier transform infrared spectroscopy (FT-IR) demonstrated a remarkable change upon the complexation of PAR with HSA...
June 3, 2017: Colloids and Surfaces. B, Biointerfaces
Akira Naito, Nobuaki Matsumori, Ayyalusamy Ramamoorthy
A variety of biomolecules acting on the cell membrane folds into a biologically active structure in the membrane environment. It is, therefore, important to determine the structures and dynamics of such biomolecules in a membrane environment. While several biophysical techniques are used to obtain low-resolution information, solid-state NMR spectroscopy is one of the most powerful means for determining the structure and dynamics of membrane bound biomolecules such as antibacterial biomolecules and amyloidogenic proteins; unlike X-ray crystallography and solution NMR spectroscopy, applications of solid-state NMR spectroscopy are not limited by non-crystalline, non-soluble nature or molecular size of membrane-associated biomolecules...
June 6, 2017: Biochimica et Biophysica Acta
Katharina Root, Yves Wittwer, Konstantin Barylyuk, Ulrike Anders, Renato Zenobi
Native ESI-MS is increasingly used for quantitative analysis of biomolecular interactions. In such analyses, peak intensity ratios measured in mass spectra are treated as abundance ratios of the respective molecules in solution. While signal intensities of similar-size analytes, such as a protein and its complex with a small molecule, can be directly compared, significant distortions of the peak ratio due to unequal signal response of analytes impede the application of this approach for large oligomeric biomolecular complexes...
June 7, 2017: Journal of the American Society for Mass Spectrometry
Karin Margarita Frei, Chiara Villa, Marie Louise Jørkov, Morten E Allentoft, Flemming Kaul, Per Ethelberg, Samantha S Reiter, Andrew S Wilson, Michelle Taube, Jesper Olsen, Niels Lynnerup, Eske Willerslev, Kristian Kristiansen, Robert Frei
Establishing the age at which prehistoric individuals move away from their childhood residential location holds crucial information about the socio dynamics and mobility patterns in ancient societies. We present a novel combination of strontium isotope analyses performed on the over 3000 year old "Skrydstrup Woman" from Denmark, for whom we compiled a highly detailed month-scale model of her migration timeline. When combined with physical anthropological analyses this timeline can be related to the chronological age at which the residential location changed...
2017: PloS One
Jingcheng Hao, Ling Wang, Yitong Wang, Xiaofeng Sun, Geping Zhang, Shuli Dong
Self-assembly exploits noncovalent interactions to offer a facile and effective method for the soft materials construction with multi-functionalities and diversity. In this work, fluorescence carbon quantum dots with coordinated Ce3+ ions (CQDCe) were firstly synthesized and exploited as building blocks to generate a series of hierarchical structures via ionic self-assembly of CQDCe and biomolecules, DNA, myoglobin (Mb) and hyaluronic acid (HA). In particularly, the vesicles can be constructed by simple mixing oppositely-charged CQDCe and DNA in water...
June 4, 2017: Chemistry: a European Journal
Lisa Lautner, Kristyna Pluhackova, Nicolai K H Barth, Tilo Seydel, Wiebke Lohstroh, Rainer A Böckmann, Tobias Unruh
Neutron scattering is a powerful tool to study relaxation processes in biological membrane mimics in space and time. Combining different inelastic and quasielastic neutron scattering techniques, a large dynamic range can be covered: from atomic to mesoscopic lengths and from femto- to some hundreds of nanoseconds in time. This allows studies on e.g. the diffusion of lipids, the membrane undulation motions, the dispersion of sound waves in membranes as well as the mutual interactions of membrane constituents such as lipids, proteins, and additives...
June 1, 2017: Chemistry and Physics of Lipids
Katja Zerbe, Kerstin Moehle, John A Robinson
Protein epitope mimetics provide powerful tools to study biomolecular recognition in many areas of chemical biology. They may also provide access to new biologically active molecules and potentially to new classes of drug and vaccine candidates. Here we highlight approaches for the design of folded, structurally defined epitope mimetics, by incorporating backbone and side chains of hot residues onto a stable constrained scaffold. Using robust synthetic methods, the structural, biological, and physical properties of epitope mimetics can be optimized, by variation of both side chain and backbone chemistry...
June 1, 2017: Accounts of Chemical Research
Maria Flynn, Kali Amelia Heale, Laleh Alisaraie
Tamoxifen is an estrogen modulator that acts to competitively inhibit the binding of endogenous estrogens. It is widely used for treatment of breast cancer; however, analogous with many antineoplastic agents, tamoxifen is associated with numerous adverse effects, most prominently nausea. We have identified several off-target receptors of tamoxifen and 22 of its metabolites that include histamine H1 and H3, and muscarinic M1, M4, and M5 subtypes, and dopamine D2 receptor. We have shown how they are associated with tamoxifen and its metabolites' toxicity through a comprehensive computational analysis of their interaction modes, which were also compared to that of the related endogenous substrates of each receptor...
June 14, 2017: Chemical Research in Toxicology
Ruxi Qi, Wesley M Botello-Smith, Ray Luo
Electrostatic interactions play crucial roles in biophysical processes such as protein folding and molecular recognition. Poisson-Boltzmann equation (PBE)-based models have emerged as widely used in modeling these important processes. Though great efforts have been put into developing efficient PBE numerical models, challenges still remain due to the high dimensionality of typical biomolecular systems. In this study, we implemented and analyzed commonly used linear PBE solvers for the ever-improving graphics processing units (GPU) for biomolecular simulations, including both standard and preconditioned conjugate gradient (CG) solvers with several alternative preconditioners...
June 7, 2017: Journal of Chemical Theory and Computation
Qinglin Hu, Xuan Bai, Guoqing Hu, Yi Y Zuo
The growing risk of human exposure to airborne nanoparticles (NPs) causes a general concern on the biosafety of nanotechnology. Inhaled NPs can deposit in the deep lung at which they interact with the pulmonary surfactant (PS). Despite the increasing study of nano-bio interactions, detailed molecular mechanisms by which inhaled NPs interact with the natural PS system remain unclear. Using coarse-grained molecular dynamics simulation, we studied the interaction between NPs and the PS system in the alveolar fluid...
May 31, 2017: ACS Nano
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