Protein structure analysisPROTEIN
STRUCTURE ANALYSIS
Analysis tools
sequential assignment NMR
soft laser spray desorption mass spectrometry
electrospray ionization mass spectrometry
Primary structure
amino acid replacement (AAR)
mutein [from mutant-protein] : a name suggested for a protein arising
as a result of a mutation; it is analogous to the wild-type protein but
does not necessarily have the same enzymological, immunological, or physicochemical
properties
block
box
repeat (e.g. C1, C2, ...)
sequence motif (motif descriptor)
consensus sequence
weight matrix
profile
Subsecondary structure
loop (1-100 amino acids) : they don't adopt secondary structure
but only conformations ...
w conformation (6÷16 residues)
Secondary structure
helix (right- or left-handed ; nN notation)
a helix(3,613)
310 helix
p helix (4,415)
w helix (4, ?)
sheet
b sheet (pleated)
mixed
parallel b-strand
antiparallel b-strand
b-bulges : it contains discontinuities
(reverse) turn : 180° reversion within 4 residues, i.e. within
a Ci-Ci+3 distance < 7 Å)
coil
Supersecondary structure orstructure motif (more
than 1 different secondary structure in contiguity) : if it found in at
least 3 heterologous proteins, it is called superfold.
bab : b-loop-helix-loop-b
adjacent b-strands
non adjacent b-strands
b-arch : b-coil-b
b-sandwich (e.g. in FHA, PDZ)
hairpin
a-hairpin : a-loop-a
b-hairpin : b-loop-b
(e.g. in ANK)
b-barrel : (b)n
(e.g. in PH, SH3). The outer membranes of mitochondria
and chloroplasts
are distinguished by the presence of b-barrel
membrane proteins. The outer
membrane of Gram-negative bacteria
also harbours b-barrel proteins. In mitochondria
these proteins fulfil a variety of functions such as transport of small
molecules (porin/VDAC), translocation of proteins (Tom40) and regulation
of mitochondrial morphology (Mdm10). These proteins are encoded by the
nucleus, synthesized in the cytosol, targeted to mitochondria as chaperone-bound
species, recognized by the translocase of the outer membrane, and then
inserted into the outer membrane where they assemble into functional oligomers.
Whereas some knowledge has been accumulated on the pathways of insertion
of proteins that span cellular membranes with a-helical
segments, very little is known about how b-barrel
proteins are integrated into lipid bilayers and assembled into oligomeric
structures. Important elements of the topogenesis of mitochondrial outer
membrane b-barrel proteins (TOB) have been conserved
during the evolution of mitochondria from endosymbiotic bacterial ancestors.
b-helix : b
Greek key : (b-strand)2 (e.g.
in DD, DED, CARD)
b-prism : (antiparallel b-strand)3
orthogonal
aligned
b-propellor : (antiparallel b-strand)4÷8
HMG box : (a-helix)3
b-trefoil : (b-hairpin)3
HLH and bHLH
4-helices bundle (e.g. in Bromo)
5-helices bundle (e.g. in SAM)
Jelly or swiss roll : (Greek key)4 = (b-strand)8
Leu zipper (LZ/bLZ, ZIP)
Rossmann fold or mononucleotide-binding motif : (babab)antiparallel
meander : (b-strand)3
Zn finger (ZF, ZnF, Znf)
C4 : 2 fronting a-helices with 2 Cys
residues each (e.g. in intracellular receptors (GR, ...), PK-C)
C2 : 2 Cys residues on a b-strand and
2 Cys residues on a fronting a-helix (e.g in
RING, TFIIIA, TDF)
7TM (e.g. in GPCRs)
HTH
Tertiary structure
domain : compact globular structure composed
of one section of a polypeptide chain that constitutes a recognizable unit
of the tertiary structure of a protein. Domains may fold up independently
and maintain their native conformation when the connecting sections of
the chain are broken. It may arise from ...
contiguous regions that fold autonomously (module)
non contiguous regions
functional analysis of binding sites :
active or catalytic sites
non-allosteric sites
DNA-binding sites (in major groove) :
LZ (e.g. in GCN4, c-Jun, c-Fos, c-Myc)
HMG (e.g. in UBF)
b (e.g. in TFIID)
HLH (e.g. in MyoD, c-Myc, Scute)
HTH (e.g. in homeodomain-containing proteins, CRP, Cro, cI, Trp-operon
repressor)
ZF (e.g. in GR, TFIIIA, Tramtrack, Hunchback, Kruppel, Snail)
allosteric site
in structural proteins
specificity sites (e.g. EF-hand in Ca2+-binding proteins)
in enzymes
specificity sites
activity sites (e.g. Rossmann fold)
kringle domain : a cysteine-rich, triply disulfide-bonded sequence
of amino acids folded into a characteristic shape resembling the looped
Scandinavian pastry; such domains occur in plasminogen and contain the
binding sites for fibrin. Similar domains are found in other proteins
and chloroplasts
Copyright © 2001-2005 Daniele Focosi.
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