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https://www.readbyqxmd.com/read/28399656/teaching-old-dyes-new-tricks-biological-probes-built-from-fluoresceins-and-rhodamines
#1
Luke D Lavis
Small-molecule fluorophores, such as fluorescein and rhodamine derivatives, are critical tools in modern biochemical and biological research. The field of chemical dyes is old; colored molecules were first discovered in the 1800s, and the fluorescein and rhodamine scaffolds have been known for over a century. Nevertheless, there has been a renaissance in using these dyes to create tools for biochemistry and biology. The application of modern chemistry, biochemistry, molecular genetics, and optical physics to these old structures enables and drives the development of novel, sophisticated fluorescent dyes...
April 7, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28375705/the-solution-assembly-of-biological-molecules-using-ion-mobility-methods-from-amino-acids-to-amyloid-%C3%AE-protein
#2
Christian Bleiholder, Michael T Bowers
Ion mobility spectrometry-mass spectrometry (IMS-MS) methods are increasingly used to study noncovalent assemblies of peptides and proteins. This review focuses on the noncovalent self-assembly of amino acids and peptides, systems at the heart of the amyloid process that play a central role in a number of devastating diseases. Three different systems are discussed in detail: the 42-residue peptide amyloid-β42 implicated in the etiology of Alzheimer's disease, several amyloid-forming peptides with 6-`11 residues, and the assembly of individual amino acids...
March 24, 2017: Annual Review of Analytical Chemistry
https://www.readbyqxmd.com/read/28375703/chemical-and-biological-dynamics-using-droplet-based-microfluidics
#3
Oliver Dressler, Xavier Casadevall I Solvas, Andrew J deMello
Recent years have witnessed an increased use of droplet-based microfluidic techniques in a wide variety of chemical and biological assays. Nevertheless, obtaining dynamic data from these platforms has remained challenging, as this often requires reading the same droplets (possibly thousands of them) multiple times over a wide range of intervals (from milliseconds to hours). In this review, we introduce the elemental techniques for the formation and manipulation of microfluidic droplets, together with the most recent developments in these areas...
March 24, 2017: Annual Review of Analytical Chemistry
https://www.readbyqxmd.com/read/28375702/beyond-antibodies-as-binding-partners-the-role-of-antibody-mimetics-in-bioanalysis
#4
Xiaowen Yu, Yu-Ping Yang, Emre Dikici, Sapna K Deo, Sylvia Daunert
The emergence of novel binding proteins or antibody mimetics capable of binding to ligand analytes in a manner analogous to that of the antigen-antibody interaction has spurred increased interest in the biotechnology and bioanalytical communities. The goal is to produce antibody mimetics designed to outperform antibodies with regard to binding affinities, cellular and tumor penetration, large-scale production, and temperature and pH stability. The generation of antibody mimetics with tailored characteristics involves the identification of a naturally occurring protein scaffold as a template that binds to a desired ligand...
March 24, 2017: Annual Review of Analytical Chemistry
https://www.readbyqxmd.com/read/28375701/light-addressable-potentiometric-sensors-for-quantitative-spatial-imaging-of-chemical-species
#5
Tatsuo Yoshinobu, Ko-Ichiro Miyamoto, Carl Frederik Werner, Arshak Poghossian, Torsten Wagner, Michael J Schöning
A light-addressable potentiometric sensor (LAPS) is a semiconductor-based chemical sensor, in which a measurement site on the sensing surface is defined by illumination. This light addressability can be applied to visualize the spatial distribution of pH or the concentration of a specific chemical species, with potential applications in the fields of chemistry, materials science, biology, and medicine. In this review, the features of this chemical imaging sensor technology are compared with those of other technologies...
March 27, 2017: Annual Review of Analytical Chemistry
https://www.readbyqxmd.com/read/28375690/ultrafast-x-ray-crystallography-and-liquidography
#6
Hosung Ki, Key Young Oang, Jeongho Kim, Hyotcherl Ihee
Time-resolved X-ray diffraction provides direct information on three-dimensional structures of reacting molecules and thus can be used to elucidate structural dynamics of chemical and biological reactions. In this review, we discuss time-resolved X-ray diffraction on small molecules and proteins with particular emphasis on its application to crystalline (crystallography) and liquid-solution (liquidography) samples. Time-resolved X-ray diffraction has been used to study picosecond and slower dynamics at synchrotrons and can now access even femtosecond dynamics with the recent arrival of X-ray free-electron lasers...
March 27, 2017: Annual Review of Physical Chemistry
https://www.readbyqxmd.com/read/28369976/quantum-chemical-calculations-of-tryptophan-%C3%A2-heme-electron-and-excitation-energy-transfer-rates-in-myoglobin
#7
Christian J Suess, Jonathan D Hirst, Nicholas A Besley
The development of optical multidimensional spectroscopic techniques has opened up new possibilities for the study of biological processes. Recently, ultrafast two-dimensional ultraviolet spectroscopy experiments have determined the rates of tryptophan → heme electron transfer and excitation energy transfer for the two tryptophan residues in myoglobin (Consani et al., Science, 2013, 339, 1586). Here, we show that accurate prediction of these rates can be achieved using Marcus theory in conjunction with time-dependent density functional theory...
April 1, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28301759/ice-surfaces
#8
Mary Jane Shultz
Ice is a fundamental solid with important environmental, biological, geological, and extraterrestrial impact. The stable form of ice at atmospheric pressure is hexagonal ice, Ih Despite its prevalence, Ih remains an enigmatic solid, in part due to challenges in preparing samples for fundamental studies. Surfaces of ice present even greater challenges. Recently developed methods for preparation of large single-crystal samples make it possible to reproducibly prepare any chosen face to address numerous fundamental questions...
March 15, 2017: Annual Review of Physical Chemistry
https://www.readbyqxmd.com/read/28301758/phospholipid-bilayers-stability-and-encapsulation-of-nanoparticles
#9
Elnaz Alipour, Duncan Halverson, Samantha McWhirter, Gilbert C Walker
Nanoparticles are widely studied for their potential medical uses in diagnostics and therapeutics. The interface between a nanoparticle and its target has been a focus of research, both to guide the nanoparticle and to prevent it from deactivating. Given nature's frequent use of phospholipid vesicles as carriers, much attention has been paid to phospholipids as a vehicle for drug delivery. The physical chemistry of bilayer formation and nanoparticle encapsulation is complex, touching on fundamental properties of hydrophobicity...
March 15, 2017: Annual Review of Physical Chemistry
https://www.readbyqxmd.com/read/28301754/bioanalytical-measurements-enabled-by-surface-enhanced-raman-scattering-sers-probes
#10
Lauren E Jamieson, Steven M Asiala, Kirsten Gracie, Karen Faulds, Duncan Graham
Since its discovery in 1974, surface-enhanced Raman scattering (SERS) has gained momentum as an important tool in analytical chemistry. SERS is used widely for analysis of biological samples, ranging from in vitro cell culture models, ex vivo tissue and blood samples, and direct in vivo application. New insights have been gained into biochemistry, with an emphasis on biomolecule detection, from small molecules such as glucose and amino acids to larger biomolecules such as DNA, proteins, and lipids. These measurements have increased our understanding of biological systems, and significantly, they have improved diagnostic capabilities...
February 23, 2017: Annual Review of Analytical Chemistry
https://www.readbyqxmd.com/read/28301749/sizing-up-protein-ligand-complexes-the-rise-of-structural-mass-spectrometry-approaches-in-the-pharmaceutical-sciences
#11
Joseph D Eschweiler, Richard Kerr, Jessica Rabuck-Gibbons, Brandon T Ruotolo
Capturing the dynamic interplay between proteins and their myriad interaction partners is critically important for advancing our understanding of almost every biochemical process and human disease. The importance of this general area has spawned many measurement methods capable of assaying such protein complexes, and the mass spectrometry-based structural biology methods described in this review form an important part of that analytical arsenal. Here, we survey the basic principles of such measurements, cover recent applications of the technology that have focused on protein-small-molecule complexes, and discuss the bright future awaiting this group of technologies...
March 15, 2017: Annual Review of Analytical Chemistry
https://www.readbyqxmd.com/read/28301748/single-molecule-arrays-for-protein-and-nucleic-acid-analysis
#12
Limor Cohen, David R Walt
The last few years have seen breakthroughs that will transform our ability to measure important analytes. Miniaturization of reaction volumes and confinement of analytes of interest into ultrasmall containers have greatly enhanced the sensitivity and throughput of many detection methods. Fabrication of microwell arrays and implementation of bead-based assays have been instrumental in the development of methods for measuring relevant biomolecules, with applications to both diagnostics and fundamental biological studies...
March 15, 2017: Annual Review of Analytical Chemistry
https://www.readbyqxmd.com/read/28301747/single-cell-transcriptional-analysis
#13
Angela R Wu, Jianbin Wang, Aaron M Streets, Yanyi Huang
Despite being a relatively recent technological development, single-cell transcriptional analysis through high-throughput sequencing has already been used in hundreds of fruitful studies to make exciting new biological discoveries that would otherwise be challenging or even impossible. Consequently, this has fueled a virtuous cycle of even greater interest in the field and compelled development of further improved technical methodologies and approaches. Thanks to the combined efforts of the research community, including the fields of biochemistry and molecular biology, technology and instrumentation, data science, computational biology, and bioinformatics, the single-cell RNA-sequencing field is advancing at a pace that is both astounding and unprecedented...
March 16, 2017: Annual Review of Analytical Chemistry
https://www.readbyqxmd.com/read/28301745/applications-of-surface-second-harmonic-generation-in-biological-sensing
#14
Renee J Tran, Krystal L Sly, John C Conboy
Surface second harmonic generation (SHG) is a coherent, nonlinear optical technique that is well suited for investigations of biomolecular interactions at interfaces. SHG is surface specific due to the intrinsic symmetry constraints on the nonlinear process, providing a distinct analytical advantage over linear spectroscopic methods, such as fluorescence and UV-Visible absorbance spectroscopies. SHG has the ability to detect low concentrations of analytes, such as proteins, peptides, and small molecules, due to its high sensitivity, and the second harmonic response can be enhanced through the use of target molecules that are resonant with the incident (ω) and/or second harmonic (2ω) frequencies...
March 16, 2017: Annual Review of Analytical Chemistry
https://www.readbyqxmd.com/read/28301728/coupling-front-end-separations-ion-mobility-spectrometry-and-mass-spectrometry-for-enhanced-multidimensional-biological-and-environmental-analyses
#15
Xueyun Zheng, Roza Wojcik, Xing Zhang, Yehia M Ibrahim, Kristin E Burnum-Johnson, Daniel J Orton, Matthew E Monroe, Ronald J Moore, Richard D Smith, Erin S Baker
Ion mobility spectrometry (IMS) is a widely used analytical technique for rapid molecular separations in the gas phase. Though IMS alone is useful, its coupling with mass spectrometry (MS) and front-end separations is extremely beneficial for increasing measurement sensitivity, peak capacity of complex mixtures, and the scope of molecular information available from biological and environmental sample analyses. In fact, multiple disease screening and environmental evaluations have illustrated that the IMS-based multidimensional separations extract information that cannot be acquired with each technique individually...
February 23, 2017: Annual Review of Analytical Chemistry
https://www.readbyqxmd.com/read/28226222/computer-simulations-of-intrinsically-disordered-proteins
#16
Song-Ho Chong, Prathit Chatterjee, Sihyun Ham
The investigation of intrinsically disordered proteins (IDPs) is a new frontier in structural and molecular biology that requires a new paradigm to connect structural disorder to function. Molecular dynamics simulations and statistical thermodynamics potentially offer ideal tools for atomic-level characterizations and thermodynamic descriptions of this fascinating class of proteins that will complement experimental studies. However, IDPs display sensitivity to inaccuracies in the underlying molecular mechanics force fields...
February 6, 2017: Annual Review of Physical Chemistry
https://www.readbyqxmd.com/read/28125288/at-the-intersection-of-chemistry-biology-and-medicine
#17
Christopher T Walsh
After an undergraduate degree in biology at Harvard, I started graduate school at The Rockefeller Institute for Medical Research in New York City in July 1965. I was attracted to the chemical side of biochemistry and joined Fritz Lipmann's large, hierarchical laboratory to study enzyme mechanisms. That work led to postdoctoral research with Robert Abeles at Brandeis, then a center of what, 30 years later, would be called chemical biology. I spent 15 years on the Massachusetts Institute of Technology faculty, in both the Chemistry and Biology Departments, and then 26 years on the Harvard Medical School Faculty...
January 11, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/27991680/toward-amino-acid-typing-for-proteins-in-fflux
#18
Timothy L Fletcher, Paul L A Popelier
Continuing the development of the FFLUX, a multipolar polarizable force field driven by machine learning, we present a modern approach to atom-typing and building transferable models for predicting atomic properties in proteins. Amino acid atomic charges in a peptide chain respond to the substitution of a neighboring residue and this response can be categorized in a manner similar to atom-typing. Using a machine learning method called kriging, we are able to build predictive models for an atom that is defined, not only by its local environment, but also by its neighboring residues, for a minimal additional computational cost...
March 5, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/27868210/computing-infrared-spectra-of-proteins-using-the-exciton-model
#19
Fouad S Husseini, David Robinson, Neil T Hunt, Anthony W Parker, Jonathan D Hirst
The ability to compute from first principles the infrared spectrum of a protein in solution phase representing a biological system would provide a useful connection to atomistic models of protein structure and dynamics. Indeed, such calculations are a vital complement to 2DIR experimental measurements, allowing the observed signals to be interpreted in terms of detailed structural and dynamical information. In this article, we have studied nine structurally and spectroscopically well-characterized proteins, representing a range of structural types...
November 21, 2016: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/27761512/data-on-the-purification-and-crystallization-of-the-loss-of-function-von-willebrand-disease-variant-p-gly1324ser-of-the-von-willebrand-factor-a1-domain
#20
James C Campbell, Alexander Tischer, Venkata Machha, Laurie Moon-Tasson, Banumathi Sankaran, Choel Kim, Matthew Auton
von Willebrand factor׳s (VWF) primary hemostatic responsibility is to deposit platelets at sites of vascular injury to prevent bleeding. This function is mediated by the interaction between the VWF A1 domain and the constitutively active platelet receptor, GPIbα. The crystal structure of the A1 domain harboring the von Willebrand disease (vWD) type 2M mutation p.Gly1324Ser has been recently published in the Journal of Biological Chemistry describing its effect on the function and structural stability of the A1 domain of VWF, "Mutational constraints on local unfolding inhibit the rheological adaptation of von Willebrand factor" [1]...
June 2016: Data in Brief
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