Native state
Encyclopedia
In biochemistry
, the native state of a protein
is its operative or functional form. While all protein molecules begin as simple unbranched chains of amino acids, once completed they assume highly specific three-dimensional shapes; that ultimate shape, known as tertiary structure
, is the folded shape that possesses a minimum of free energy
. It is a protein's tertiary, folded structure that makes it capable of performing its biological function. In fact, shape changes in proteins are the primary cause of several neurodegenerative diseases, including those caused by prion
s and amyloid
(ie. mad cow disease, kuru, Creutzfeld-Jakob disease).
Many enzyme
s and other non-structural protein
s have more than one native state, and they operate or undergo regulation by transitioning between these states. However, "native state" is used almost exclusively in the singular, typically to distinguish properly folded
proteins from denatured
or unfolded ones. In other contexts, the folded shape of a protein is most often referred to as its native "conformation" or "structure."
Folded and unfolded proteins are often easily distinguished by virtue of their water solubilities, as many proteins become insoluble on denaturation. Proteins in the native state will have defined secondary structure
, which can be detected spectroscopically, by circular dichroism
and by nuclear magnetic resonance (NMR).
The native state of a protein can be distinguished from a molten globule
, by among other things, distances measured by NMR. Amino acids widely separated in a protein's sequence
may touch or lie very close to one another within a stably folded protein. In a molten globule, on the other hand, their time-averaged distances are liable to be greater.
Learning how native state proteins can be manufactured is important, as attempts to create proteins from scratch have resulted in molten globules and not true native state products. Therefore, an understanding of the native state is crucial in protein engineering
.
's crust are oxides or sulfides, and as such do not manifest the properties of refined metals. Occasionally, however, metals are found in uncombined metallic forms, in varying degrees of purity. These "metals found as metals" are referred to as being in their "native state". For example, Native copper
.
Biochemistry
Biochemistry, sometimes called biological chemistry, is the study of chemical processes in living organisms, including, but not limited to, living matter. Biochemistry governs all living organisms and living processes...
, the native state of a protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
is its operative or functional form. While all protein molecules begin as simple unbranched chains of amino acids, once completed they assume highly specific three-dimensional shapes; that ultimate shape, known as tertiary structure
Tertiary structure
In biochemistry and molecular biology, the tertiary structure of a protein or any other macromolecule is its three-dimensional structure, as defined by the atomic coordinates.-Relationship to primary structure:...
, is the folded shape that possesses a minimum of free energy
Thermodynamic free energy
The thermodynamic free energy is the amount of work that a thermodynamic system can perform. The concept is useful in the thermodynamics of chemical or thermal processes in engineering and science. The free energy is the internal energy of a system less the amount of energy that cannot be used to...
. It is a protein's tertiary, folded structure that makes it capable of performing its biological function. In fact, shape changes in proteins are the primary cause of several neurodegenerative diseases, including those caused by prion
Prion
A prion is an infectious agent composed of protein in a misfolded form. This is in contrast to all other known infectious agents which must contain nucleic acids . The word prion, coined in 1982 by Stanley B. Prusiner, is a portmanteau derived from the words protein and infection...
s and amyloid
Amyloid
Amyloids are insoluble fibrous protein aggregates sharing specific structural traits. Abnormal accumulation of amyloid in organs may lead to amyloidosis, and may play a role in various neurodegenerative diseases.-Definition:...
(ie. mad cow disease, kuru, Creutzfeld-Jakob disease).
Many enzyme
Enzyme
Enzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process, called substrates, are converted into different molecules, called products. Almost all chemical reactions in a biological cell need enzymes in order to occur at rates...
s and other non-structural protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
s have more than one native state, and they operate or undergo regulation by transitioning between these states. However, "native state" is used almost exclusively in the singular, typically to distinguish properly folded
Protein folding
Protein folding is the process by which a protein structure assumes its functional shape or conformation. It is the physical process by which a polypeptide folds into its characteristic and functional three-dimensional structure from random coil....
proteins from denatured
Denaturation (biochemistry)
Denaturation is a process in which proteins or nucleic acids lose their tertiary structure and secondary structure by application of some external stress or compound, such as a strong acid or base, a concentrated inorganic salt, an organic solvent , or heat...
or unfolded ones. In other contexts, the folded shape of a protein is most often referred to as its native "conformation" or "structure."
Folded and unfolded proteins are often easily distinguished by virtue of their water solubilities, as many proteins become insoluble on denaturation. Proteins in the native state will have defined secondary structure
Secondary structure
In biochemistry and structural biology, secondary structure is the general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids...
, which can be detected spectroscopically, by circular dichroism
Circular dichroism
Circular dichroism refers to the differential absorption of left and right circularly polarized light. This phenomenon was discovered by Jean-Baptiste Biot, Augustin Fresnel, and Aimé Cotton in the first half of the 19th century. It is exhibited in the absorption bands of optically active chiral...
and by nuclear magnetic resonance (NMR).
The native state of a protein can be distinguished from a molten globule
Molten globule
The term molten globule was first coined by A. Wada and M Ohgushi in 1983. It was first found 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...
, by among other things, distances measured by NMR. Amino acids widely separated in a protein's sequence
Primary structure
The primary structure of peptides and proteins refers to the linear sequence of its amino acid structural units. The term "primary structure" was first coined by Linderstrøm-Lang in 1951...
may touch or lie very close to one another within a stably folded protein. In a molten globule, on the other hand, their time-averaged distances are liable to be greater.
Learning how native state proteins can be manufactured is important, as attempts to create proteins from scratch have resulted in molten globules and not true native state products. Therefore, an understanding of the native state is crucial in protein engineering
Protein engineering
Protein engineering is the process of developing useful or valuable proteins. It is a young discipline, with much research taking place into the understanding of protein folding and recognition for protein design principles....
.
Metallurgy
With respect to metals: the term native state refers to metals which are found chemically uncombined in nature. Most usable metallic ores in the EarthEarth
Earth is the third planet from the Sun, and the densest and fifth-largest of the eight planets in the Solar System. It is also the largest of the Solar System's four terrestrial planets...
's crust are oxides or sulfides, and as such do not manifest the properties of refined metals. Occasionally, however, metals are found in uncombined metallic forms, in varying degrees of purity. These "metals found as metals" are referred to as being in their "native state". For example, Native copper
Native copper
Copper, as native copper, is one of the few metallic elements to occur in uncombined form as a natural mineral, although most commonly occurs in oxidized states and mixed with other elements...
.