modular structure of proteins

Question 1

Motifs and domains

Answer 1

Simple secondary structures fold combine to form structural motifs or larger functional domains

Independent order of structure 

Commonly found and conserved across functionally related proteins

Question 2

Motifs

Answer 2

Combination of two or more secondary structures to form a recognizable folded arrangement

Organized or combined into larger structural and functional domains 

EF hand is a motif which allows the binding of Ca2+ 

Resembles a helix turn helix 

Greek key motif: 

Consists of antiparallel beta strands 

Forms easily during protein folding process  

Therefore common and generally isn’t associated with a specific function 

Beta barrel: 

Beta strand wrap around to form circular tunnel

Question 3

Domains

Answer 3

Complex structure at the tertiary or quaternary level often involving interactions between distant parts of a protein or motifs

Question 4

Globin domain

Answer 4

Each chain of HB has a very similar tertiary structure to a single myoglobin chain

This strongly suggests evolution from a common ancestral O2 binding polypeptide

Question 5

DNA binding motifs

Answer 5

Helices can be inserted into the major groove of DNA in a sequence specific matter

Amino acid sequence of a DNA binding motif provides specificity

Question 6

DNA binding motifs (Helix loop helix)

Answer 6

Found in some transcription factors

Central portion is made from overlapping helices that form a structure enabling dimerization 

Larger helix contains the DNA binding regions 

Terminal part of the lower opposing helices contain basic amino acids that interact with the major groove of the DNA – giving rise to b/HLH functional domain

Question 7

DNA binding motifs (Leucine zipper)

Answer 7

Formed from 2 contiguous alpha helices and is a dimeric protein formed from two polypeptide chains

Dimers zip together in the top stalk to form a short coiled coil 

Coil held together by hydrophobic interactions down opposing sides of the helix 

Basic amino acid dominate lower part of the helix and interact with the DNA major groove 

Heterodimersation expands the regulatory potential of leucine zippers

Question 8

DNA binding motifs (Helix turn helix)

Answer 8

Two short helices orientated at right angles to each other and connected by a turn

Motif found in both eukaryotic and prokaryotic DNA binding proteins 

CRO is a homodomer 

Recognizes palindromic sequence and by binding DNA represses transcription 

Only recognition helix interacts with nucleotide sequence and locates within the major groove

Question 9

DNA binding motifs (zinc finger)

Answer 9

Alpha helix and beta sheet held together by non-covalent interactions with zinc

Alpha helix of each motif interacts with the major groove of DNA and recognizes a specific DNA sequence 

Present in many hormone receptors