Protein structureProtein structure is the three-dimensional arrangement of atoms in an amino acid-chain molecule. Proteins are polymers - specifically polypeptides - formed from sequences of amino acids, which are the monomers of the polymer. A single amino acid monomer may also be called a residue, which indicates a repeating unit of a polymer. Proteins form by amino acids undergoing condensation reactions, in which the amino acids lose one water molecule per reaction in order to attach to one another with a peptide bond.
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.
Random coilIn polymer chemistry, a random coil is a conformation of polymers where the monomer subunits are oriented randomly while still being bonded to adjacent units. It is not one specific shape, but a statistical distribution of shapes for all the chains in a population of macromolecules. The conformation's name is derived from the idea that, in the absence of specific, stabilizing interactions, a polymer backbone will "sample" all possible conformations randomly.
Small-angle neutron scatteringSmall-angle neutron scattering (SANS) is an experimental technique that uses elastic neutron scattering at small scattering angles to investigate the structure of various substances at a mesoscopic scale of about 1–100 nm. Small angle neutron scattering is in many respects very similar to small-angle X-ray scattering (SAXS); both techniques are jointly referred to as small-angle scattering (SAS).
Biomolecular structureBiomolecular structure is the intricate folded, three-dimensional shape that is formed by a molecule of protein, DNA, or RNA, and that is important to its function. The structure of these molecules may be considered at any of several length scales ranging from the level of individual atoms to the relationships among entire protein subunits. This useful distinction among scales is often expressed as a decomposition of molecular structure into four levels: primary, secondary, tertiary, and quaternary.
Conformational changeProtein dynamics In biochemistry, a conformational change is a change in the shape of a macromolecule, often induced by environmental factors. A macromolecule is usually flexible and dynamic. Its shape can change in response to changes in its environment or other factors; each possible shape is called a conformation, and a transition between them is called a conformational change. Factors that may induce such changes include temperature, pH, voltage, light in chromophores, concentration of ions, phosphorylation, or the binding of a ligand.
Protein tertiary structureProtein tertiary structure is the three dimensional shape of a protein. The tertiary structure will have a single polypeptide chain "backbone" with one or more protein secondary structures, the protein domains. Amino acid side chains may interact and bond in a number of ways. The interactions and bonds of side chains within a particular protein determine its tertiary structure. The protein tertiary structure is defined by its atomic coordinates. These coordinates may refer either to a protein domain or to the entire tertiary structure.
Conformational ensemblesIn computational chemistry, conformational ensembles, also known as structural ensembles, are experimentally constrained computational models describing the structure of intrinsically unstructured proteins. Such proteins are flexible in nature, lacking a stable tertiary structure, and therefore cannot be described with a single structural representation. The techniques of ensemble calculation are relatively new on the field of structural biology, and are still facing certain limitations that need to be addressed before it will become comparable to classical structural description methods such as biological macromolecular crystallography.
Topological insulatorA topological insulator is a material whose interior behaves as an electrical insulator while its surface behaves as an electrical conductor, meaning that electrons can only move along the surface of the material. A topological insulator is an insulator for the same reason a "trivial" (ordinary) insulator is: there exists an energy gap between the valence and conduction bands of the material. But in a topological insulator, these bands are, in an informal sense, "twisted", relative to a trivial insulator.
Nucleic acid secondary structureNucleic acid secondary structure is the basepairing interactions within a single nucleic acid polymer or between two polymers. It can be represented as a list of bases which are paired in a nucleic acid molecule. The secondary structures of biological DNAs and RNAs tend to be different: biological DNA mostly exists as fully base paired double helices, while biological RNA is single stranded and often forms complex and intricate base-pairing interactions due to its increased ability to form hydrogen bonds stemming from the extra hydroxyl group in the ribose sugar.
Phase transitionIn chemistry, thermodynamics, and other related fields, a phase transition (or phase change) is the physical process of transition between one state of a medium and another. Commonly the term is used to refer to changes among the basic states of matter: solid, liquid, and gas, and in rare cases, plasma. A phase of a thermodynamic system and the states of matter have uniform physical properties. During a phase transition of a given medium, certain properties of the medium change as a result of the change of external conditions, such as temperature or pressure.
Eclipsed conformationIn chemistry an eclipsed conformation is a conformation in which two substituents X and Y on adjacent atoms A, B are in closest proximity, implying that the torsion angle X–A–B–Y is 0°. Such a conformation can exist in any open chain, single chemical bond connecting two sp3-hybridised atoms, and it is normally a conformational energy maximum. This maximum is often explained by steric hindrance, but its origins sometimes actually lie in hyperconjugation (as when the eclipsing interaction is of two hydrogen atoms).
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.
Conformational isomerismIn chemistry, conformational isomerism is a form of stereoisomerism in which the isomers can be interconverted just by rotations about formally single bonds (refer to figure on single bond rotation). While any two arrangements of atoms in a molecule that differ by rotation about single bonds can be referred to as different conformations, conformations that correspond to local minima on the potential energy surface are specifically called conformational isomers or conformers.
Topological orderIn physics, topological order is a kind of order in the zero-temperature phase of matter (also known as quantum matter). Macroscopically, topological order is defined and described by robust ground state degeneracy and quantized non-Abelian geometric phases of degenerate ground states. Microscopically, topological orders correspond to patterns of long-range quantum entanglement. States with different topological orders (or different patterns of long range entanglements) cannot change into each other without a phase transition.
Coil–globule transitionIn polymer physics, the coil–globule transition is the collapse of a macromolecule from an expanded coil state through an ideal coil state to a collapsed globule state, or vice versa. The coil–globule transition is of importance in biology due to the presence of coil-globule transitions in biological macromolecules such as proteins and DNA. It is also analogous with the swelling behavior of a crosslinked polymer gel and is thus of interest in biomedical engineering for controlled drug delivery.
CopolymerIn polymer chemistry, a copolymer is a polymer derived from more than one species of monomer. The polymerization of monomers into copolymers is called copolymerization. Copolymers obtained from the copolymerization of two monomer species are sometimes called bipolymers. Those obtained from three and four monomers are called terpolymers and quaterpolymers, respectively. Copolymers can be characterized by a variety of techniques such as NMR spectroscopy and size-exclusion chromatography to determine the molecular size, weight, properties, and composition of the material.
Neutron scatteringNeutron scattering, the irregular dispersal of free neutrons by matter, can refer to either the naturally occurring physical process itself or to the man-made experimental techniques that use the natural process for investigating materials. The natural/physical phenomenon is of elemental importance in nuclear engineering and the nuclear sciences. Regarding the experimental technique, understanding and manipulating neutron scattering is fundamental to the applications used in crystallography, physics, physical chemistry, biophysics, and materials research.
PolystyrenePolystyrene (PS) ˌpɒliˈstaɪriːn is a synthetic polymer made from monomers of the aromatic hydrocarbon styrene. Polystyrene can be solid or foamed. General-purpose polystyrene is clear, hard, and brittle. It is an inexpensive resin per unit weight. It is a poor barrier to oxygen and water vapor and has a relatively low melting point. Polystyrene is one of the most widely used plastics, with the scale of its production being several million tonnes per year. Polystyrene is naturally transparent, but can be colored with colorants.
Nucleic acid structureNucleic acid structure refers to the structure of nucleic acids such as DNA and RNA. Chemically speaking, DNA and RNA are very similar. Nucleic acid structure is often divided into four different levels: primary, secondary, tertiary, and quaternary. Nucleic acid sequence Primary structure consists of a linear sequence of nucleotides that are linked together by phosphodiester bond. It is this linear sequence of nucleotides that make up the primary structure of DNA or RNA.
