While these initiatives have all added value to the scientific articles in which they have been involved, they have been experimental prototypes, have depended on specific software or operating system requirements that have not been supported over the passage of time, or have provided supplementary information, not the main content of an article. More recently, Biochemical Journal and ACS Chemical Biology have hosted a number of papers with interactive figures and animations as supporting materials. In the mid-1990s, Chemical Communications acted as a test bed for a variety of new web technologies supporting enhanced and interactive figures, implemented by the CLIC Consortium (Murray-Rust et al., 1997 ). In 1993, the journal Protein Science published a CD-ROM containing the entire contents of its first volume of publication, the entire contents of the Protein Data Bank, and copies of MAGE and PREKIN software for creating and viewing `kinemages', annotated interactive views of three-dimensional protein structures (Richardson & Richardson, 1992 ). Organic Chemistry With a Biological Emphasis by Tim Soderberg (University of Minnesota, Morris)ĭr.The use of molecular graphics visualization software in association with journal articles reporting or describing crystal and molecular structures is not new.
Jmol first glance code#
(x-ray crystallographic data are from Protein Science 1999, 8, 291 pdb code 4ALD. Shown below is an image of the glycolytic enzyme fructose-1,6-bisphosphate aldolase (in grey), with the substrate molecule bound inside the active site pocket.
For example, we saw in the introduction to this chapter that the TrpVI receptor in mammalian tissues binds capsaicin (from hot chili peppers) in its binding pocket and initiates a heat/pain signal which is sent to the brain. Receptors are proteins that bind specifically to one or more molecules - referred to as ligands - to initiate a biochemical process. One or more reacting molecules - often called substrates - become bound in the active site pocket of an enzyme, where the actual reaction takes place. It is this shape of this folded structure, and the precise arrangement of the functional groups within the structure (especially in the area of the binding pocket) that determines the function of the protein.Įnzymes are proteins which catalyze biochemical reactions. Once a protein polymer is constructed, it in many cases folds up very specifically into a three-dimensional structure, which often includes one or more 'binding pockets' in which other molecules can be bound. Thus we might refer to the 'glutamate residue' at position 3 of the CHEM peptide above. When an amino acid is incorporated into a protein it loses a molecule of water and what remains is called a residue of the original amino acid. Using the single-letter code, the sequence is abbreviated CHEM. Below is a four amino acid peptide with the sequence "cysteine - histidine - glutamate - methionine". Protein sequences are written in the amino terminal (N-terminal) to carboxylate terminal (C-terminal) direction, with either three-letter or single-letter abbreviations for the amino acids (see amino acid table). Which amino acids are linked, and in what order - the protein sequence - is what distinguishes one protein from another, and is coded for by an organism's DNA. Proteins (polymers of ~50 amino acids or more) and peptides (shorter polymers) are formed when the amino group of one amino acid monomer reacts with the carboxylate carbon of another amino acid to form an amide linkage, which in protein terminology is a peptide bond. The two 'hooks' on an amino acid monomer are the amine and carboxylate groups. Many amino acid side chains contain a functional group (the side chain of serine, for example, contains a primary alcohol), while others, like alanine, lack a functional group, and contain only a simple alkane. There are twenty different side chains in naturally occurring amino acids, and it is the identity of the side chain that determines the identity of the amino acid: for example, if the side chain is a -CH 3 group, the amino acid is alanine, and if the side chain is a -CH 2OH group, the amino acid is serine. An amino acid can be thought of as having two components: a 'backbone', or 'main chain', composed of an ammonium group, an 'alpha-carbon', and a carboxylate, and a variable 'side chain' (in green below) bonded to the alpha-carbon. Proteins are polymers of amino acids, linked by amide groups known as peptide bonds.