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 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.
Representation theoryRepresentation theory is a branch of mathematics that studies abstract algebraic structures by representing their elements as linear transformations of vector spaces, and studies modules over these abstract algebraic structures. In essence, a representation makes an abstract algebraic object more concrete by describing its elements by matrices and their algebraic operations (for example, matrix addition, matrix multiplication).
Group representationIn the mathematical field of representation theory, group representations describe abstract groups in terms of bijective linear transformations of a vector space to itself (i.e. vector space automorphisms); in particular, they can be used to represent group elements as invertible matrices so that the group operation can be represented by matrix multiplication. In chemistry, a group representation can relate mathematical group elements to symmetric rotations and reflections of molecules.
Irreducible representationIn mathematics, specifically in the representation theory of groups and algebras, an irreducible representation or irrep of an algebraic structure is a nonzero representation that has no proper nontrivial subrepresentation , with closed under the action of . Every finite-dimensional unitary representation on a Hilbert space is the direct sum of irreducible representations. Irreducible representations are always indecomposable (i.e. cannot be decomposed further into a direct sum of representations), but the converse may not hold, e.
Molecular dynamicsMolecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of the system. In the most common version, the trajectories of atoms and molecules are determined by numerically solving Newton's equations of motion for a system of interacting particles, where forces between the particles and their potential energies are often calculated using interatomic potentials or molecular mechanical force fields.
Lie algebra representationIn the mathematical field of representation theory, a Lie algebra representation or representation of a Lie algebra is a way of writing a Lie algebra as a set of matrices (or endomorphisms of a vector space) in such a way that the Lie bracket is given by the commutator. In the language of physics, one looks for a vector space together with a collection of operators on satisfying some fixed set of commutation relations, such as the relations satisfied by the angular momentum operators.
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.
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.
Protein quaternary structureProtein quaternary structure is the fourth (and highest) classification level of protein structure. Protein quaternary structure refers to the structure of proteins which are themselves composed of two or more smaller protein chains (also referred to as subunits). Protein quaternary structure describes the number and arrangement of multiple folded protein subunits in a multi-subunit complex. It includes organizations from simple dimers to large homooligomers and complexes with defined or variable numbers of subunits.
