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Protein structure databases are critical for many efforts in computational biology such as structure based drug design, both in developing the computational methods used and in providing a large experimental dataset used by some methods to provide insights about the function of a protein. [34]
Discovering the tertiary structure of a protein, or the quaternary structure of its complexes, can provide important clues about how the protein performs its function and how it can be affected, i.e. in drug design. As proteins are too small to be seen under a light microscope, other methods have to be employed to determine their structure.
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 different proteins.
At the top level are all alpha proteins (domains consisting of alpha helices), all beta proteins (domains consisting of beta sheets), and mixed alpha helix/beta sheet proteins. While most proteins adopt a single stable fold, a few proteins can rapidly interconvert between one or more folds. These are referred to as metamorphic proteins. [5]
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. Peptides can also be synthesized in the ...
The structure of a protein, such as an enzyme, may change upon binding of its natural ligands, for example a cofactor. In this case, the structure of the protein bound to the ligand is known as holo structure, while the unbound protein has an apo structure. [8]
Computational techniques such as molecular dynamics simulations can be used in conjunction with empirical structure determination strategies to extend and study protein structure, conformation and function. [6] Hemoglobin, the oxygen transporting protein found in red blood cells Examples of protein structures from the Protein Data Bank (PDB)
Three-dimensional structure of a protein. Structural bioinformatics is the branch of bioinformatics that is related to the analysis and prediction of the three-dimensional structure of biological macromolecules such as proteins, RNA, and DNA.
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