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A protein contact map represents the distance between all possible amino acid residue pairs of a three-dimensional protein structure using a binary two-dimensional matrix. For two residues and , the element of the matrix is 1 if the two residues are closer than a predetermined threshold, and 0 otherwise. Various contact definitions have been ...
Protein 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.
Pyruvate kinase, a protein with three domains (In molecular biology, a protein domain is a region of a protein's polypeptide chain that is self-stabilizing and that folds independently from the rest. Each domain forms a compact folded three-dimensional structure. Many proteins consist of several domains, and a domain may appear in a variety of ...
Protein primary structure is the linear sequence of amino acids in a peptide or protein. [1] By convention, the primary structure of a protein is reported starting from the amino -terminal (N) end to the carboxyl -terminal (C) end. Protein biosynthesis is most commonly performed by ribosomes in cells.
In structural biology, a protein subunit is a polypeptide chain or single protein molecule that assembles (or " coassembles ") with others to form a protein complex. [1][2][3] Large assemblies of proteins such as viruses often use a small number of types of protein subunits as building blocks. [4]
Protein secondary structure is the local spatial conformation of the polypeptide backbone excluding the side chains. [1] The two most common secondary structural elements are alpha helices and beta sheets, though beta turns and omega loops occur as well. Secondary structure elements typically spontaneously form as an intermediate before the ...
Nucleoporins are a family of proteins which are the constituent building blocks of the nuclear pore complex (NPC). [1] The nuclear pore complex is a massive structure embedded in the nuclear envelope at sites where the inner and outer nuclear membranes fuse, forming a gateway that regulates the flow of macromolecules between the cell nucleus and the cytoplasm.
In biology literature, the term topology is also used to refer to mutual orientation of regular secondary structures, such as alpha-helices and beta strands in protein structure [3] [1]. For example, two adjacent interacting alpha-helices or beta-strands can go in the same or in opposite directions. Topology diagrams of different proteins with ...