Flashcards: Protein structure

Denaturation is a process in which proteins or nucleic acids lose the quaternary structure, 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), radiation or heat.

The alpha helix (α-helix) is a common motif in the secondary structure of proteins and is a righthand-coiled or spiral conformation (helix) in which every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid located three or four residues earlier along the protein sequence.

Ubiquitin is a small (8.5 kDa) regulatory protein that has been found in almost all tissues (ubiquitously) of eukaryotic organisms.

A dihedral angle is the angle between two intersecting planes.

In biochemistry and structural biology, protein secondary structure is the general three-dimensional form of local segments of proteins.

The term protein tertiary structure refers to a protein's geometric shape.

Rosetta@home is a distributed computing project for protein structure prediction on the Berkeley Open Infrastructure for Network Computing (BOINC) platform, run by the Baker laboratory at the University of Washington.

X-ray crystallography is a tool used for identifying the atomic and molecular structure of a crystal, in which the crystalline atoms cause a beam of incident X-rays to diffract into many specific directions.

Nucleotide pyrophosphatase/phosphodiesterase (NPP) is a class of dimeric enzymes that catalyze the hydrolysis of phosphate diester bonds.

Circular dichroism (CD) is dichroism involving circularly polarized light, i.

The L27 domain is a protein domain that is found in receptor targeting proteins Lin-2 and Lin-7 (LIN7A, LIN7B, LIN7C), as well as some protein kinases and human MPP2 protein.

Intelectins are lectins (carbohydrate-binding proteins) expressed in humans and other chordates.

Voltage sensitive phosphatases or voltage sensor-containing phosphatases, commonly abbreviated VSPs, are a protein family found in many species, including humans, mice, zebrafish, frogs, and sea squirt.

A cystine knot is a protein structural motif containing three disulfide bridges (formed from pairs of cysteine residues).

In chemistry and biology a disulfide refers to a functional group with the general structure R–S–S–R'.

Nuclear magnetic resonance spectroscopy of proteins (usually abbreviated protein NMR) is a field of structural biology in which NMR spectroscopy is used to obtain information about the structure and dynamics of proteins, and also nucleic acids, and their complexes.

Conformational entropy is the entropy associated with the number of conformations of a molecule.

Macromolecular structure validation is the process of evaluating reliability for 3-dimensional atomic models of large biological molecules such as proteins and nucleic acids.

Guanidinium chloride or guanidine hydrochloride, usually abbreviated GdmCl and sometimes GdnHCl or GuHCl, is the hydrochloride salt of guanidine.

Caspase recruitment domains, or Caspase activation and recruitment domains (CARDs), are interaction motifs found in a wide array of proteins, typically those involved in processes relating to inflammation and apoptosis.