Native stateIn biochemistry, the native state of a protein or nucleic acid is its properly folded and/or assembled form, which is operative and functional. The native state of a biomolecule may possess all four levels of biomolecular structure, with the secondary through quaternary structure being formed from weak interactions along the covalently-bonded backbone. This is in contrast to the denatured state, in which these weak interactions are disrupted, leading to the loss of these forms of structure and retaining only the biomolecule's primary structure.
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.
Protein foldingProtein 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.
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).
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.
Thermodynamic equationsThermodynamics is expressed by a mathematical framework of thermodynamic equations which relate various thermodynamic quantities and physical properties measured in a laboratory or production process. Thermodynamics is based on a fundamental set of postulates, that became the laws of thermodynamics. One of the fundamental thermodynamic equations is the description of thermodynamic work in analogy to mechanical work, or weight lifted through an elevation against gravity, as defined in 1824 by French physicist Sadi Carnot.
Folding funnelThe folding funnel hypothesis is a specific version of the energy landscape theory of protein folding, which assumes that a protein's native state corresponds to its free energy minimum under the solution conditions usually encountered in cells. Although energy landscapes may be "rough", with many non-native local minima in which partially folded proteins can become trapped, the folding funnel hypothesis assumes that the native state is a deep free energy minimum with steep walls, corresponding to a single well-defined tertiary structure.
Globular proteinIn biochemistry, globular proteins or spheroproteins are spherical ("globe-like") proteins and are one of the common protein types (the others being fibrous, disordered and membrane proteins). Globular proteins are somewhat water-soluble (forming colloids in water), unlike the fibrous or membrane proteins. There are multiple fold classes of globular proteins, since there are many different architectures that can fold into a roughly spherical shape. The term globin can refer more specifically to proteins including the globin fold.
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.
Thermodynamic equilibriumThermodynamic equilibrium is an axiomatic concept of thermodynamics. It is an internal state of a single thermodynamic system, or a relation between several thermodynamic systems connected by more or less permeable or impermeable walls. In thermodynamic equilibrium, there are no net macroscopic flows of matter nor of energy within a system or between systems. In a system that is in its own state of internal thermodynamic equilibrium, no macroscopic change occurs.
Thermodynamic systemA thermodynamic system is a body of matter and/or radiation, considered as separate from its surroundings, and studied using the laws of thermodynamics. Thermodynamic systems may be isolated, closed, or open. An isolated system exchanges no matter or energy with its surroundings, whereas a closed system does not exchange matter but may exchange heat and experience and exert forces. An open system can interact with its surroundings by exchanging both matter and energy.
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.
ProteinProteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, responding to stimuli, providing structure to cells and organisms, and transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes, and which usually results in protein folding into a specific 3D structure that determines its activity.
Molten globuleIn molecular biology, the term molten globule (MG) refers to protein states that are more or less compact (hence the "globule"), but are lacking the specific tight packing of amino acid residues which creates the solid state-like tertiary structure of completely folded proteins. It was found, for example, in cytochrome c, which conserves a native-like secondary structure content but without the tightly packed protein interior, under low pH and high salt concentration.
Thermodynamic processClassical thermodynamics considers three main kinds of thermodynamic process: (1) changes in a system, (2) cycles in a system, and (3) flow processes. (1)A Thermodynamic process is a process in which the thermodynamic state of a system is changed. A change in a system is defined by a passage from an initial to a final state of thermodynamic equilibrium. In classical thermodynamics, the actual course of the process is not the primary concern, and often is ignored.
Thermodynamic stateIn thermodynamics, a thermodynamic state of a system is its condition at a specific time; that is, fully identified by values of a suitable set of parameters known as state variables, state parameters or thermodynamic variables. Once such a set of values of thermodynamic variables has been specified for a system, the values of all thermodynamic properties of the system are uniquely determined. Usually, by default, a thermodynamic state is taken to be one of thermodynamic equilibrium.
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.
EntropyEntropy is a scientific concept, as well as a measurable physical property, that is most commonly associated with a state of disorder, randomness, or uncertainty. The term and the concept are used in diverse fields, from classical thermodynamics, where it was first recognized, to the microscopic description of nature in statistical physics, and to the principles of information theory.
Protein designProtein design is the rational design of new protein molecules to design novel activity, behavior, or purpose, and to advance basic understanding of protein function. Proteins can be designed from scratch (de novo design) or by making calculated variants of a known protein structure and its sequence (termed protein redesign). Rational protein design approaches make protein-sequence predictions that will fold to specific structures.
Fibrous proteinIn molecular biology, fibrous proteins or scleroproteins are one of the three main classifications of protein structure (alongside globular and membrane proteins). Fibrous proteins are made up of elongated or fibrous polypeptide chains which form filamentous and sheet-like structures. These kind of protein can be distinguished from globular protein by its low solubility in water. Such proteins serve protective and structural roles by forming connective tissue, tendons, bone matrices, and muscle fiber.
