Alpha helixAn alpha helix (or α-helix) is a sequence of amino acids in a protein that are twisted into a coil (a helix). The alpha helix is the most common structural arrangement in the secondary structure of proteins. It is also the most extreme type of local structure, and it is the local structure that is most easily predicted from a sequence of amino acids. The alpha helix has a right hand-helix conformation in which every backbone N−H group hydrogen bonds to the backbone C=O group of the amino acid that is four residues earlier in the protein sequence.
Protein secondary structureProtein secondary structure is the local spatial conformation of the polypeptide backbone excluding the side chains. The two most common secondary structural elements are alpha helices and beta sheets, though beta turns and omega loops occur as well. Secondary structure elements typically spontaneously form as an intermediate before the protein folds into its three dimensional tertiary structure. Secondary structure is formally defined by the pattern of hydrogen bonds between the amino hydrogen and carboxyl oxygen atoms in the peptide backbone.
Spin–spin relaxationIn physics, the spin–spin relaxation is the mechanism by which Mxy, the transverse component of the magnetization vector, exponentially decays towards its equilibrium value in nuclear magnetic resonance (NMR) and magnetic resonance imaging (MRI). It is characterized by the spin–spin relaxation time, known as T2, a time constant characterizing the signal decay. It is named in contrast to T1, the spin–lattice relaxation time.
Protein dynamicsProteins 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.
Glass transitionThe glass–liquid transition, or glass transition, is the gradual and reversible transition in amorphous materials (or in amorphous regions within semicrystalline materials) from a hard and relatively brittle "glassy" state into a viscous or rubbery state as the temperature is increased. An amorphous solid that exhibits a glass transition is called a glass. The reverse transition, achieved by supercooling a viscous liquid into the glass state, is called vitrification.
Relaxation (physics)In the physical sciences, relaxation usually means the return of a perturbed system into equilibrium. Each relaxation process can be categorized by a relaxation time τ. The simplest theoretical description of relaxation as function of time t is an exponential law exp(−t/τ) (exponential decay). Let the homogeneous differential equation: model damped unforced oscillations of a weight on a spring. The displacement will then be of the form . The constant T () is called the relaxation time of the system and the constant μ is the quasi-frequency.
Activation energyIn chemistry and physics, activation energy is the minimum amount of energy that must be provided for compounds to result in a chemical reaction. The activation energy (Ea) of a reaction is measured in joules per mole (J/mol), kilojoules per mole (kJ/mol) or kilocalories per mole (kcal/mol). Activation energy can be thought of as the magnitude of the potential barrier (sometimes called the energy barrier) separating minima of the potential energy surface pertaining to the initial and final thermodynamic state.
Specific heat capacityIn thermodynamics, the specific heat capacity (symbol c) of a substance is the heat capacity of a sample of the substance divided by the mass of the sample, also sometimes referred to as massic heat capacity. Informally, it is the amount of heat that must be added to one unit of mass of the substance in order to cause an increase of one unit in temperature. The SI unit of specific heat capacity is joule per kelvin per kilogram, J⋅kg−1⋅K−1.
Heat capacityHeat capacity or thermal capacity is a physical property of matter, defined as the amount of heat to be supplied to an object to produce a unit change in its temperature. The SI unit of heat capacity is joule per kelvin (J/K). Heat capacity is an extensive property. The corresponding intensive property is the specific heat capacity, found by dividing the heat capacity of an object by its mass. Dividing the heat capacity by the amount of substance in moles yields its molar heat capacity.
Hydrogen bondIn chemistry, a hydrogen bond (or H-bond) is a primarily electrostatic force of attraction between a hydrogen (H) atom which is covalently bound to a more electronegative "donor" atom or group (Dn), and another electronegative atom bearing a lone pair of electrons—the hydrogen bond acceptor (Ac). Such an interacting system is generally denoted , where the solid line denotes a polar covalent bond, and the dotted or dashed line indicates the hydrogen bond.
Self-assembly of nanoparticlesNanoparticles are classified as having at least one of three dimensions be in the range of 1-100 nm. The small size of nanoparticles allows them to have unique characteristics which may not be possible on the macro-scale. Self-assembly is the spontaneous organization of smaller subunits to form larger, well-organized patterns. For nanoparticles, this spontaneous assembly is a consequence of interactions between the particles aimed at achieving a thermodynamic equilibrium and reducing the system’s free energy.
Heat capacity ratioIn thermal physics and thermodynamics, the heat capacity ratio, also known as the adiabatic index, the ratio of specific heats, or Laplace's coefficient, is the ratio of the heat capacity at constant pressure (CP) to heat capacity at constant volume (CV). It is sometimes also known as the isentropic expansion factor and is denoted by γ (gamma) for an ideal gas or κ (kappa), the isentropic exponent for a real gas. The symbol γ is used by aerospace and chemical engineers.
DielectricIn electromagnetism, a dielectric (or dielectric medium) is an electrical insulator that can be polarised by an applied electric field. When a dielectric material is placed in an electric field, electric charges do not flow through the material as they do in an electrical conductor, because they have no loosely bound, or free, electrons that may drift through the material, but instead they shift, only slightly, from their average equilibrium positions, causing dielectric polarisation.
Molar heat capacityThe molar heat capacity of a chemical substance is the amount of energy that must be added, in the form of heat, to one mole of the substance in order to cause an increase of one unit in its temperature. Alternatively, it is the heat capacity of a sample of the substance divided by the amount of substance of the sample; or also the specific heat capacity of the substance times its molar mass. The SI unit of molar heat capacity is joule per kelvin per mole, J⋅K−1⋅mol−1.
Dielectric spectroscopyDielectric spectroscopy (which falls in a subcategory of impedance spectroscopy) measures the dielectric properties of a medium as a function of frequency. It is based on the interaction of an external field with the electric dipole moment of the sample, often expressed by permittivity. It is also an experimental method of characterizing electrochemical systems. This technique measures the impedance of a system over a range of frequencies, and therefore the frequency response of the system, including the energy storage and dissipation properties, is revealed.
Protein fold classIn molecular biology, protein fold classes are broad categories of protein tertiary structure topology. They describe groups of proteins that share similar amino acid and secondary structure proportions. Each class contains multiple, independent protein superfamilies (i.e. are not necessarily evolutionarily related to one another). Four large classes of protein that are generally agreed upon by the two main structure classification databases (SCOP and CATH).
Self-assemblySelf-assembly is a process in which a disordered system of pre-existing components forms an organized structure or pattern as a consequence of specific, local interactions among the components themselves, without external direction. When the constitutive components are molecules, the process is termed molecular self-assembly. Self-assembly can be classified as either static or dynamic. In static self-assembly, the ordered state forms as a system approaches equilibrium, reducing its free energy.
Beta sheetThe beta sheet, (β-sheet) (also β-pleated sheet) is a common motif of the regular protein secondary structure. Beta sheets consist of beta strands (β-strands) connected laterally by at least two or three backbone hydrogen bonds, forming a generally twisted, pleated sheet. A β-strand is a stretch of polypeptide chain typically 3 to 10 amino acids long with backbone in an extended conformation. The supramolecular association of β-sheets has been implicated in the formation of the fibrils and protein aggregates observed in amyloidosis, Alzheimer's disease and other proteinopathies.
Arrhenius equationIn physical chemistry, the Arrhenius equation is a formula for the temperature dependence of reaction rates. The equation was proposed by Svante Arrhenius in 1889, based on the work of Dutch chemist Jacobus Henricus van 't Hoff who had noted in 1884 that the van 't Hoff equation for the temperature dependence of equilibrium constants suggests such a formula for the rates of both forward and reverse reactions. This equation has a vast and important application in determining the rate of chemical reactions and for calculation of energy of activation.
Quasistatic processIn thermodynamics, a quasi-static process (also known as a quasi-equilibrium process.the Latin quasi, meaning ‘as if’), is a thermodynamic process that happens slowly enough for the system to remain in internal physical (but not necessarily chemical) thermodynamic equilibrium. An example of this is quasi-static expansion of a mixture of hydrogen and oxygen gas, where the volume of the system changes so slowly that the pressure remains uniform throughout the system at each instant of time during the process.
