Related Research Articles
Phospholipids are a class of lipids whose molecule has a hydrophilic "head" containing a phosphate group and two hydrophobic "tails" derived from fatty acids, joined by an alcohol residue. Marine phospholipids typically have omega-3 fatty acids EPA and DHA integrated as part of the phospholipid molecule. The phosphate group can be modified with simple organic molecules such as choline, ethanolamine or serine.
Protein folding is the physical process where a protein chain is translated into its native three-dimensional structure, typically a "folded" conformation, by which the protein becomes biologically functional. Via an expeditious and reproducible process, a polypeptide folds into its characteristic three-dimensional structure from a random coil. Each protein exists first as an unfolded polypeptide or random coil after being translated from a sequence of mRNA into a linear chain of amino acids. At this stage, the polypeptide lacks any stable three-dimensional structure. As the polypeptide chain is being synthesized by a ribosome, the linear chain begins to fold into its three-dimensional structure.
Surface science is the study of physical and chemical phenomena that occur at the interface of two phases, including solid–liquid interfaces, solid–gas interfaces, solid–vacuum interfaces, and liquid–gas interfaces. It includes the fields of surface chemistry and surface physics. Some related practical applications are classed as surface engineering. The science encompasses concepts such as heterogeneous catalysis, semiconductor device fabrication, fuel cells, self-assembled monolayers, and adhesives. Surface science is closely related to interface and colloid science. Interfacial chemistry and physics are common subjects for both. The methods are different. In addition, interface and colloid science studies macroscopic phenomena that occur in heterogeneous systems due to peculiarities of interfaces.
A biosensor is an analytical device, used for the detection of a chemical substance, that combines a biological component with a physicochemical detector. The sensitive biological element, e.g. tissue, microorganisms, organelles, cell receptors, enzymes, antibodies, nucleic acids, etc., is a biologically derived material or biomimetic component that interacts with, binds with, or recognizes the analyte under study. The biologically sensitive elements can also be created by biological engineering. The transducer or the detector element, which transforms one signal into another one, works in a physicochemical way: optical, piezoelectric, electrochemical, electrochemiluminescence etc., resulting from the interaction of the analyte with the biological element, to easily measure and quantify. The biosensor reader device connects with the associated electronics or signal processors that are primarily responsible for the display of the results in a user-friendly way. This sometimes accounts for the most expensive part of the sensor device, however it is possible to generate a user friendly display that includes transducer and sensitive element. The readers are usually custom-designed and manufactured to suit the different working principles of biosensors.
Optical coherence tomography (OCT) is an imaging technique that uses interferometry with short-coherence-length light to obtain micrometer-level depth resolution and uses transverse scanning of the light beam to form two- and three-dimensional images from light reflected from within biological tissue or other scattering media. Short-coherence-length light can be obtained using a superluminescent diode (SLD) with a broad spectral bandwidth or a broadly tunable laser with narrow linewidth. The first demonstration of OCT imaging was published by a team from MIT and Harvard Medical School in a 1991 article in the journal Science. The article introduced the term "OCT" to credit its derivation from optical coherence-domain reflectometry, in which the axial resolution is based on temporal coherence. The first demonstrations of in vivo OCT imaging quickly followed.
Surface plasmon resonance (SPR) is a phenomenon that occurs where electrons in a thin metal sheet become excited by light that is directed to the sheet with a particular angle of incidence, and then travel parallel to the sheet. Assuming a constant light source wavelength and that the metal sheet is thin, the angle of incidence that triggers SPR is related to the refractive index of the material and even a small change in the refractive index will cause SPR to not be observed. This makes SPR a possible technique for detecting particular substances (analytes) and SPR biosensors have been developed to detect various important biomarkers.
In biochemistry and pharmacology, a ligand is a substance that forms a complex with a biomolecule to serve a biological purpose. The etymology stems from Latin ligare, which means 'to bind'. In protein-ligand binding, the ligand is usually a molecule which produces a signal by binding to a site on a target protein. The binding typically results in a change of conformational isomerism (conformation) of the target protein. In DNA-ligand binding studies, the ligand can be a small molecule, ion, or protein which binds to the DNA double helix. The relationship between ligand and binding partner is a function of charge, hydrophobicity, and molecular structure.
In biochemistry, a conformational change is a change in the shape of a macromolecule, often induced by environmental factors.
Nucleic acid methods are the techniques used to study nucleic acids: DNA and RNA.
Protein–lipid interaction is the influence of membrane proteins on the lipid physical state or vice versa.
A model lipid bilayer is any bilayer assembled in vitro, as opposed to the bilayer of natural cell membranes or covering various sub-cellular structures like the nucleus. They are used to study the fundamental properties of biological membranes in a simplified and well-controlled environment, and increasingly in bottom-up synthetic biology for the construction of artificial cells. A model bilayer can be made with either synthetic or natural lipids. The simplest model systems contain only a single pure synthetic lipid. More physiologically relevant model bilayers can be made with mixtures of several synthetic or natural lipids.
Carbohydrate–protein interactions are the intermolecular and intramolecular interactions between protein and carbohydrate moieties. These interactions form the basis of specific recognition of carbohydrates by lectins. Carbohydrates are important biopolymers and have a variety of functions. Often carbohydrates serve a function as a recognition element. That is, they are specifically recognized by other biomolecules. Proteins which bind carbohydrate structures are known as lectins. Compared to the study of protein–protein and protein–DNA interaction, it is relatively recent that scientists get to know the protein–carbohydrate binding.
In biochemistry, the conformation–activity relationship is the relationship between the biological activity and the chemical structure or conformational changes of a biomolecule. This terminology emphasizes the importance of dynamic conformational changes for the biological function, rather than the importance of static three-dimensional structure used in the analysis of structure–activity relationships.
Bio-layer interferometry (BLI) is an optical biosensing technology that analyzes biomolecular interactions in real-time without the need for fluorescent labeling. Alongside Surface Plasmon Resonance, BLI is one of few widely available label-free biosensing technologies, a detection style that yields more information in less time than traditional processes. The technology relies on the phase shift-wavelength correlation created between interference patterns off of two unique surfaces on the tip of a biosensor. BLI has significant applications in quantifying binding strength, measuring protein interactions, and identifying properties of reaction kinetics, such as rate constants and reaction rates.
Within surface science, a quartz crystal microbalance with dissipation monitoring (QCM-D) is a type of quartz crystal microbalance (QCM) based on the ring-down technique. It is used in interfacial acoustic sensing. Its most common application is the determination of a film thickness in a liquid environment. It can be used to investigate further properties of the sample, most notably the layer's softness.
There are many methods to investigate protein–protein interactions which are the physical contacts of high specificity established between two or more protein molecules involving electrostatic forces and hydrophobic effects. Each of the approaches has its own strengths and weaknesses, especially with regard to the sensitivity and specificity of the method. A high sensitivity means that many of the interactions that occur are detected by the screen. A high specificity indicates that most of the interactions detected by the screen are occurring in reality.
Surface plasmon resonance microscopy (SPRM), also called surface plasmon resonance imaging (SPRI), is a label free analytical tool that combines the surface plasmon resonance of metallic surfaces with imaging of the metallic surface. The heterogeneity of the refractive index of the metallic surface imparts high contrast images, caused by the shift in the resonance angle. SPRM can achieve a sub-nanometer thickness sensitivity and lateral resolution achieves values of micrometer scale. SPRM is used to characterize surfaces such as self-assembled monolayers, multilayer films, metal nanoparticles, oligonucleotide arrays, and binding and reduction reactions. Surface plasmon polaritons are surface electromagnetic waves coupled to oscillating free electrons of a metallic surface that propagate along a metal/dielectric interface. Since polaritons are highly sensitive to small changes in the refractive index of the metallic material, it can be used as a biosensing tool that does not require labeling. SPRM measurements can be made in real-time, such as measuring binding kinetics of membrane proteins in single cells, or DNA hybridization.
Multi-parametric surface plasmon resonance (MP-SPR) is based on surface plasmon resonance (SPR), an established real-time label-free method for biomolecular interaction analysis, but it uses a different optical setup, a goniometric SPR configuration. While MP-SPR provides same kinetic information as SPR, it provides also structural information. Hence, MP-SPR measures both surface interactions and nanolayer properties.
Alireza Mashaghi is a physician-scientist and biophysicist at Leiden University. He is known for his contributions to single-molecule analysis of chaperone assisted protein folding, molecular topology and medical systems biophysics and bioengineering. He is a leading advocate for interdisciplinary research and education in medicine and pharmaceutical sciences.
Grating-coupled interferometry (GCI) is a biophysical characterization method mainly used in biochemistry and drug discovery for label-free analysis of molecular interactions. Similar to other optical methods such as surface plasmon resonance (SPR) or bio-layer interferometry (BLI), it is based on measuring refractive index changes within an evanescent field near a sensor surface. After immobilizing a target to the sensor surface, analyte molecules in solution which bind to that target cause a small increase in local refractive index. By monitoring these refractive changes over time characteristics such as kinetic rates and affinity constants of the analyte-target binding, or analyte concentrations, can be determined.
References
- ↑ Cross, G; Reeves, AA; Brand, S; Popplewell, JF; Peel, LL; Swann, MJ; Freeman, NJ (2003). "A new quantitative optical biosensor for protein characterisation". Biosensors and Bioelectronics . 19 (4): 383–90. doi:10.1016/S0956-5663(03)00203-3. PMID 14615097.
- ↑ Swann, MJ; Freeman, NJ; Cross, GH (2007). "Dual Polarization Interferometry: A Real-Time Optical Technique for Measuring (Bio)Molecular Orientation, Structure and Function at the Solid/Liquid Interface". In Marks, R.S.; Lowe, C.R.; Cullen, D.C.; Weetall, H.H.; Karube, I. (eds.). Handbook of Biosensors and Biochips. Vol. 1. Wiley. Pt. 4, Ch. 33, pp. 549–568. ISBN 978-0-470-01905-4.
- ↑ Coffey, Paul D.; Swann, Marcus J.; Waigh, Thomas A.; Schedin, Fred; Lu, Jian R. (June 22, 2009). "Multiple path length dual polarization interferometry". Optics Express. 17 (13): 10959. doi: 10.1364/OE.17.010959 .
- ↑ Coffey, Paul. "Interfacial Measurements of Colloidal and Bio-colloidal Systems in Real-Time" . Retrieved December 16, 2022.
- ↑ Delivopoulos, Evangelos; Ouberai, Myriam M.; Coffey, Paul D.; Swann, Marcus J.; Shakesheff, Kevin M.; Welland, Mark E. (February 2015). "Serum protein layers on parylene-C and silicon oxide: Effect on cell adhesion". Colloids and Surfaces B: Biointerfaces. 126: 169–177. doi: 10.1016/j.colsurfb.2014.12.020 . PMC 4342411 .
- ↑ Coffey, Paul David; Swann, Marcus Jack; Waigh, Thomas Andrew; Mu, Qingshan; Lu, Jian Ren (2013). "The structure and mass of heterogeneous thin films measured with dual polarization interferometry and ellipsometry". RSC Advances. 3 (10): 3316. doi:10.1039/C2RA22911K.
- ↑ Boudjemline, A; Clarke, DT; Freeman, NJ; Nicholson, JM; Jones, GR (2008). "Early stages of protein crystallization as revealed by emerging optical waveguide technology". Journal of Applied Crystallography . 41 (3): 523. doi:10.1107/S0021889808005098.
- ↑ Mashaghi, A; Swann, M; Popplewell, J; Textor, M; Reimhult, E (2008). "Optical Anisotropy of Supported Lipid Structures Probed by Waveguide Spectroscopy and Its Application to Study of Supported Lipid Bilayer Formation Kinetics". Analytical Chemistry . 80 (10): 3666–76. doi:10.1021/ac800027s. PMID 18422336.
- ↑ Sanghera, N; Swann, MJ; Ronan, G; Pinheiro, TJ (2009). "Insight into early events in the aggregation of the prion protein on lipid membranes". Biochimica et Biophysica Acta (BBA) - Biomembranes. 1788 (10): 2245–51. doi: 10.1016/j.bbamem.2009.08.005 . PMID 19703409.
- ↑ Lee, TH; Heng, C; Swann, MJ; Gehman, JD; Separovic, F; Aguilar, MI (2010). "Real-time quantitative analysis of lipid disordering by aurein 1.2 during membrane adsorption, destabilisation and lysis". Biochimica et Biophysica Acta (BBA) - Biomembranes. 1798 (10): 1977–86. doi: 10.1016/j.bbamem.2010.06.023 . PMID 20599687.
