Modular structure of proteins

Electrostatic - Carboxyl COO- and amine NH3+ Hydrogen bonding - Secondary amine NH, carbonyl C=O groups, hydroxyl OH Non-polar/hydrophobic interactions -> Hydrocarbon Covalent boding - Disulphide bonds

A pattern of amino acids that are found in related genes or proteins

Minimum arrangement of independently forming secondary structures combining recognisable folds across many different proteins Or A combination of two or more secondary structures to form a recognisable localised folded arrangement of structure

Domains more clearly define a functional unit than a motif but both are evolutionarily conserved and are modular in nature

A more complex structure at the tertiary or quaternary level, involving interaction between distant parts of a protein or motifs

Calcium binding motif found in e.g. calmodulin and troponin-C. Combines with calcium, two hands at either end connected by an alpha helix

Specific arrangement of beta strands forming antiparallel beta sheet

Beta strands wrapped around to form circular tunnel

Parallel strands of a beta sheet interlinked with a alpha helix to form a beta-alpha-beta motif

Modular units of function being conserved but shuffled between genes E.g. mammalian phospholipase C contains 4 different recognisable domains. These can each be found individually in other proteins

Haemoglobin chains have a similar tertiary structure to the single myoglobin chain, suggesting evolution from an ancestral oxygen binding polypeptide

The amino acid sequence of a DNA binding motif provides specificity Different DNA binding domains and motifs present the binding helix using different arrangements of the structural motif

Binds DNA only in the dimeric form Exists as hetero and homodimers Central portion made from overlapping helices Terminal part of lower opposing helices contain basic amino acids that interact with the major groove of the DNA - b/HLH functional domain

2 contiguous alpha helices and like the HLH, is a dimeric protein formed from two polypeptide chains The dimers zip together in the top stalk to form a short coiled-coil The coil is held together by hydrophobic interactions down opposing sides of the helix As in the b/HLH basic amino acids dominate the lower part of the helix and interact with the DNA major groove Heterodimerisation expands the regulatory potential of leucine zippers

Two short helices orientated at right angles to each other, connected by a turn Motif found in both prokaryotic and eukaryotic DNA binding proteins CRO protein is a homodimer CRO recognises palindromic sequence and by binding DNA represses transcription Only the recognition helix interacts with the nucleotide sequence itself and like other DNA binding motifs it locates within the major groove

Alpha helix and a beta sheet held together by non-covalent interactions with zinc Motif on polypeptide chain containing zinc atom stabilising the recognition helix and loop structure Alpha helix of each motif interacts with the major groove of DNA and recognises a specific DNA sequence