**** proteins: primary structure — secondary structure — tertiary structure — conformation — native state — protein folding — enzyme — receptor — transmembrane receptor — ion channel — membrane transporter — collagen — silk

The β sheet ( also β-pleated sheet ) is the second form of regular secondary structure in proteins, only somewhat less common than the alpha helix.

Denaturation is a process in which proteins or nucleic acids lose the tertiary structure and secondary structure which is present in their native state, by application of some external stress or compound such as a strong acid or base, a concentrated inorganic salt, an organic solvent ( e. g., alcohol or chloroform ), or heat.

* In secondary structure denaturation, proteins lose all regular repeating patterns such as alpha-helices and beta-pleated sheets, and adopt a random coil configuration.

The interaction of hormone and receptor typically triggers a cascade of secondary effects within the cytoplasm of the cell, often involving phosphorylation or dephosphorylation of various other cytoplasmic proteins, changes in ion channel permeability, or increased concentrations of intracellular molecules that may act as secondary messengers ( e. g., cyclic AMP ).

Intramolecular hydrogen bonding is partly responsible for the secondary, tertiary, and quaternary structures of proteins and nucleic acids.

Each NPC contains at least 456 individual protein molecules and is composed of 30 distinct proteins ( nucleoporins ).< ref > The other half show structural characteristics typical of " natively unfolded " proteins, i. e. they are highly flexible proteins that lack ordered secondary structure.

An intracellular pathway ( consisting of SMAD2 / SMAD3, SMAD4 and the inhibitor SMAD7 ) is responsible for the secondary messenger system that induces transcription of the proteins and enzymes responsible for collagen deposition.

In biochemistry and structural biology, secondary structure is the general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids ( DNA / RNA ).

Many adaptor proteins and enzymes activated as part of signal transduction possess specialized protein domains that bind to specific secondary messenger molecules.

Modern methods are sometimes able to predict the tertiary structure de novo to within 5 Å for small proteins (< 120 residues ) and under favorable conditions, e. g., confident secondary structure predictions.

Most notably, UV CD is used to investigate the secondary structure of proteins.

Methods for estimating secondary structure in polymers, proteins and polypeptides in particular, often require that the measured molar ellipticity spectrum be converted to a normalized value, specifically a value independent of the polymer length.

The far-UV ( ultraviolet ) CD spectrum of proteins can reveal important characteristics of their secondary structure.

Specialized trans-membrane proteins recognize the substance and allows it access ( or, in the case of secondary transport, expend energy on forcing it ) to cross the membrane when it otherwise would not, either because it is one to which the phospholipid bilayer of the membrane is impermeable or because it is moved in the direction of the concentration gradient.

The other cases, which usually derive their energy through exploitation of an electrochemical gradient, are known as secondary active transport and involve pore-forming proteins that form channels through the cell membrane.

* Alpha helix, a common motif in the secondary structure of proteins

* STRIDE ( protein ), algorithm for Structural identification of the secondary structures of proteins

SDS-PAGE ( SDS polyacrylamide gel electrophoresis ) maintains polypeptides in a denatured state once they have been treated with strong reducing agents to remove secondary and tertiary structure ( e. g. disulfide bonds to sulfhydryl groups and SH ) and thus allows separation of proteins by their molecular weight.

Export of sodium from the cell provides the driving force for several secondary active transporters membrane transport proteins, which import glucose, amino acids, and other nutrients into the cell by use of the sodium gradient.

Splicing is regulated by trans-acting proteins ( repressors and activators ), corresponding cis-acting regulatory sites ( silencers and enhancers ) on the RNA, and other RNA features that influence how splicing will occur, such as secondary structures.

The structure of proteins is traditionally described in a hierarchy of four levels.

The exact chemical composition and the sequence in which these units are arranged is called the primary structure, in the case of proteins.

It is also useful for determining the tertiary structure and quaternary structure of purified proteins, especially since it can be carried out under native solution conditions.

In eukaryotes, nuclear chromosomes are packaged by proteins into a condensed structure called chromatin.

In the nuclear chromosomes of eukaryotes, the uncondensed DNA exists in a semi-ordered structure, where it is wrapped around histones ( structural proteins ), forming a composite material called chromatin.

The local structure of chromatin during interphase depends on the genes present on the DNA: DNA coding genes that are actively transcribed (" turned on ") are more loosely packaged and are found associated with RNA polymerases ( referred to as euchromatin ) while DNA coding inactive genes (" turned off ") are found associated with structural proteins and are more tightly packaged ( heterochromatin ).

Epigenetic chemical modification of the structural proteins in chromatin also alter the local chromatin structure, in particular chemical modifications of histone proteins by methylation and acetylation.

# DNA wraps around histone proteins forming nucleosomes ; the " beads on a string " structure ( euchromatin ).

Polycomb-group proteins play a role in regulating genes through modulation of chromatin structure.

The structure of the condensed chromosome is thought to be loops of 30 nm fibre to a central scaffold of proteins.

This understanding has led to the notion that all the information needed for proteins to assume their native state was encoded in the primary structure of the protein, and hence in the DNA that codes for the protein, the so called " Anfinsen's thermodynamic hypothesis ".

The short wavelength of these matter waves makes them ideally suited to study the atomic crystal structure of solids and large molecules like proteins.

Based on the three-dimensional structure of the Rep proteins the geminiviruses and parvoviruses may be related.

This structure is also found in the catalytic domains of topoisomerase Ia, topoisomerase II, the OLD-family nucleases and DNA repair proteins related to the RecR protein.

* Chemical fixation – for biological specimens aims to stabilize the specimen's mobile macromolecular structure by chemical crosslinking of proteins with aldehydes such as formaldehyde and glutaraldehyde, and lipids with osmium tetroxide.

Bragg was influential in the effort to beat a leading American chemist, Linus Pauling, to the discovery of DNA's structure ( after having been ' pipped-at-the-post ' by Pauling's success in determining the alpha helix structure of proteins ).

Since the circulating thyroid hormones are the amino acids thyroxine and tri-iodothyronine ( cf. Section C ), it is clear that some mechanism must exist in the thyroid gland for their release from proteins before secretion.

-- Glycerinated muscle, in the presence of the physiological agent ( ATP ) responsible for delivering energy to the mechanochemically active proteins of muscle, has been shown to undergo a contraction which is highly sensitive both to temperature and to solvent composition in mixtures of alcohols and water.

The proteins and fats are burned off, and the cholesterol is left behind.

It contains no detergents but is created by whipping up proteins and lectins secreted by the female.

Amino acids have zero mobility in electrophoresis at their isoelectric point, although this behaviour is more usually exploited for peptides and proteins than single amino acids.

The process of making proteins is called translation and involves the step-by-step addition of amino acids to a growing protein chain by a ribozyme that is called a ribosome.

Non-standard amino acids that are found in proteins are formed by post-translational modification, which is modification after translation during protein synthesis.

If there are proteins left in the shell matrix, it is also possible that they can trigger an allergic ( asthmatic ) attack.

It is now known that each of the A, B, and O alleles is actually a class of multiple alleles with different DNA sequences that produce proteins with identical properties: more than 70 alleles are known at the ABO locus.

That is, whereas antigens are the " target " of antibodies, immunoglobulin-binding proteins " attack " antibodies.

An autoantigen is usually a normal protein or complex of proteins ( and sometimes DNA or RNA ) that is recognized by the immune system of patients suffering from a specific autoimmune disease.

The tip is surrounded by a band of microtubules, called the polar ring, and among the Conoidasida there is also a funnel of tubulin proteins called the conoid.

Cortisol is the main glucocorticoid under normal conditions and its actions include mobilization of fats, proteins, and carbohydrates, but it does not increase under starvation conditions.

Before the actual process of cell death is precipitated by enzymes, apoptotic signals must cause regulatory proteins to initiate the apoptosis pathway.

MAC, also called " Mitochondrial Outer Membrane Permeabilization Pore " is regulated by various proteins, such as those encoded by the mammalian Bcl-2 family of anti-apoptopic genes, the homologs of the ced-9 gene found in C. elegans.

Control of proapoptotic proteins under normal cell conditions of nonapoptotic cells is incompletely understood, but in general, Bax or Bak are activated by the activation of BH3-only proteins, part of the Bcl-2 family.

Apoptosis in HeLa cells is inhibited by proteins produced by the cell, these inhibitory proteins target retinoblastoma tumor suppressing proteins.

HPV E6 and E7 are inhibitory proteins expressed by the human papillomavirus, HPV is responsible for the formation of the cervical tumor from which HeLa cells are derived.