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Dark Proteome
The dark proteome is defined as proteins with no defined three-dimensional structure. It can not be detected or analyzed with the use of homologous modeling or analytical quantification for the molecular conformation is unknown.Perdigão, Nelson.Dark Proteome Database: Studies on Dark Proteins" Dark Proteome Database: Studies on Dark Proteins, March 27, 201910.20944/preprints201901.0198.v1/ref> Dark proteins are mostly composed of unknown unknowns History and Origin It estimated to be about 14% of the proteome in archaea and bacteria, and as much as 44–54% of the proteome in eukaryotes and viruses, is dark. The origin of these dark proteins is unclear. Large portion of the dark proteome are of viral origin. Dark protein regions are dark due to originating from unusual organisms with no sufficient close relatives in current protein databases to provide protein to protein data on sequence alignments and structure determination. Function Dark proteins are not applicable to th ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Infrared
Infrared (IR), sometimes called infrared light, is electromagnetic radiation (EMR) with wavelengths longer than those of visible light. It is therefore invisible to the human eye. IR is generally understood to encompass wavelengths from around 1 millimeter (300 GHz) to the nominal red edge of the visible spectrum, around 700 nanometers (430 THz). Longer IR wavelengths (30 μm-100 μm) are sometimes included as part of the terahertz radiation range. Almost all black-body radiation from objects near room temperature is at infrared wavelengths. As a form of electromagnetic radiation, IR propagates energy and momentum, exerts radiation pressure, and has properties corresponding to both those of a wave and of a particle, the photon. It was long known that fires emit invisible heat; in 1681 the pioneering experimenter Edme Mariotte showed that glass, though transparent to sunlight, obstructed radiant heat. In 1800 the astronomer Sir William Herschel discovered ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Mass Spectrometry
Mass spectrometry (MS) is an analytical technique that is used to measure the mass-to-charge ratio of ions. The results are presented as a ''mass spectrum'', a plot of intensity as a function of the mass-to-charge ratio. Mass spectrometry is used in many different fields and is applied to pure samples as well as complex mixtures. A mass spectrum is a type of plot of the ion signal as a function of the mass-to-charge ratio. These spectra are used to determine the elemental or isotopic signature of a sample, the masses of particles and of molecules, and to elucidate the chemical identity or structure of molecules and other chemical compounds. In a typical MS procedure, a sample, which may be solid, liquid, or gaseous, is ionized, for example by bombarding it with a beam of electrons. This may cause some of the sample's molecules to break up into positively charged fragments or simply become positively charged without fragmenting. These ions (fragments) are then separated accordin ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Single-molecule Experiment
A single-molecule experiment is an experiment that investigates the properties of individual molecules. Single-molecule studies may be contrasted with measurements on an ensemble or bulk collection of molecules, where the individual behavior of molecules cannot be distinguished, and only average characteristics can be measured. Since many measurement techniques in biology, chemistry, and physics are not sensitive enough to observe single molecules, single-molecule fluorescence techniques (that have emerged since the 1990s for probing various processes on the level of individual molecules) caused a lot of excitement, since these supplied many new details on the measured processes that were not accessible in the past. Indeed, since the 1990s, many techniques for probing individual molecules have been developed. The first single-molecule experiments were patch clamp experiments performed in the 1970s, but these were limited to studying ion channels. Today, systems investigated using s ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Wide-angle X-ray Scattering
In X-ray crystallography, wide-angle X-ray scattering (WAXS) or wide-angle X-ray diffraction (WAXD) is the analysis of Bragg peaks scattered to wide angles, which (by Bragg's law) are caused by sub-nanometer-sized structures. It is an X-ray-diffraction method and commonly used to determine a range of information about crystalline materials. The term WAXS is commonly used in polymer sciences to differentiate it from SAXS but many scientists doing "WAXS" would describe the measurements as Bragg/X-ray/powder diffraction or crystallography. Wide-angle X-ray scattering is similar to small-angle X-ray scattering (SAXS) but the increasing angle between the sample and detector is probing smaller length scales. This requires samples to be more ordered/crystalline for information to be extracted. In a dedicated SAXS instrument the distance from sample to the detector is longer to increase angular resolution. Most diffractometers can be used to perform both WAXS and limited SAXS in a single ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Small-angle X-ray Scattering
Small-angle X-ray scattering (SAXS) is a small-angle scattering technique by which nanoscale density differences in a sample can be quantified. This means that it can determine nanoparticle size distributions, resolve the size and shape of (monodisperse) macromolecules, determine pore sizes, characteristic distances of partially ordered materials, and much more. This is achieved by analyzing the elastic scattering behaviour of X-rays when travelling through the material, recording their scattering at small angles (typically 0.1 – 10°, hence the "Small-angle" in its name). It belongs to the family of small-angle scattering (SAS) techniques along with small-angle neutron scattering, and is typically done using hard X-rays with a wavelength of 0.07 – 0.2 nm.. Depending on the angular range in which a clear scattering signal can be recorded, SAXS is capable of delivering structural information of dimensions between 1 and 100 nm, and of repeat distances in partially ordered s ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Nuclear Magnetic Resonance
Nuclear magnetic resonance (NMR) is a physical phenomenon in which nuclei in a strong constant magnetic field are perturbed by a weak oscillating magnetic field (in the near field) and respond by producing an electromagnetic signal with a frequency characteristic of the magnetic field at the nucleus. This process occurs near resonance, when the oscillation frequency matches the intrinsic frequency of the nuclei, which depends on the strength of the static magnetic field, the chemical environment, and the magnetic properties of the isotope involved; in practical applications with static magnetic fields up to ca. 20 tesla, the frequency is similar to VHF and UHF television broadcasts (60–1000 MHz). NMR results from specific magnetic properties of certain atomic nuclei. Nuclear magnetic resonance spectroscopy is widely used to determine the structure of organic molecules in solution and study molecular physics and crystals as well as non-crystalline materials. ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Gel Filtration
Size-exclusion chromatography (SEC), also known as molecular sieve chromatography, is a chromatographic method in which molecules in solution are separated by their size, and in some cases molecular weight. It is usually applied to large molecules or macromolecular complexes such as proteins and industrial polymers. Typically, when an aqueous solution is used to transport the sample through the column, the technique is known as gel-filtration chromatography, versus the name gel permeation chromatography, which is used when an organic solvent is used as a mobile phase. The chromatography column is packed with fine, porous beads which are commonly composed of dextran, agarose, or polyacrylamide polymers. The pore sizes of these beads are used to estimate the dimensions of macromolecules. SEC is a widely used polymer characterization method because of its ability to provide good molar mass distribution (Mw) results for polymers. Applications The main application of gel-filtration chro ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Intrinsically Disordered Proteins
In molecular biology, an intrinsically disordered protein (IDP) is a protein that lacks a fixed or ordered three-dimensional structure, typically in the absence of its macromolecular interaction partners, such as other proteins or RNA. IDPs range from fully unstructured to partially structured and include random coil, molten globule-like aggregates, or flexible linkers in large multi-domain proteins. They are sometimes considered as a separate class of proteins along with globular, fibrous and membrane proteins. IDPs are a very large and functionally important class of proteins and their discovery has disproved the idea that three-dimensional structures of proteins must be fixed to accomplish their biological functions. For example, IDPs have been identified to participate in weak multivalent interactions that are highly cooperative and dynamic, lending them importance in DNA regulation and in cell signaling. Many IDPs can also adopt a fixed three-dimensional structure after bi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Dynamics
Proteins are generally thought to adopt unique structures determined by their amino acid sequences. However, proteins are not strictly static objects, but rather populate ensembles of (sometimes similar) conformations. Transitions between these states occur on a variety of length scales (tenths of Å to nm) and time scales (ns to s), and have been linked to functionally relevant phenomena such as allosteric signaling and enzyme catalysis. The study of protein dynamics is most directly concerned with the transitions between these states, but can also involve the nature and equilibrium populations of the states themselves. These two perspectives—kinetics and thermodynamics, respectively—can be conceptually synthesized in an "energy landscape" paradigm: highly populated states and the kinetics of transitions between them can be described by the depths of energy wells and the heights of energy barriers, respectively. Local flexibility: atoms and residues Portions of protein s ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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