Transcript aa_2

A Ala Alanine
Alanine is a small,
hydrophobic residue. Its side
chain, R, is just a methyl
group.
Alanine likes to sit in an alpha
helix, it doesn’t like beta
strands very much, but it hates
beta- turns.
If you want to mutate a
residue, but you don’t have a
good plan about what to
replace it with, take alanine
because it is a subset of all
other amino acids
©CMBI 2001
C Cys Cysteine
Cysteine is a small
hydrophobic
residue.
It doesn’t like the alpha
helix, but doesn’t mind
strands.
It can form bridges with
other cysteines (Cys-Cys
bridges).
It can bind metals
(especially Zn and Cu).
The S-H group is very
reactive and can easily be
oxidised.
©CMBI 2001
D Asp Aspartic acid
Aspartic acid, or aspartate, is
an intermediately large,
hydrophilic, negatively
charged residue. Its side
chain normally titrates at pH
4.5.
It likes to sit near the Nterminus of a helix, and in
turns. It hates strands.
It often occurs in active sites.
It can bind ions (mainly Ca).
©CMBI 2001
E Glu Glutamic
acid
Glutamic acid, or glutamate,
is a large, hydrophilic,
negatively charged residue.
Its side chain titrates at pH
4.6.
It loves the helix, doesn’t
mind being in a strand, but is
not so good for turns.
©CMBI 2001
F Phe
Phenylalanine
Phenylalanine is a large,
hydrophobic, aromatic
residue.
It is good for a strand, it
doesn’t mind sitting in a
helix, but it hates the turn.
©CMBI 2001
G Gly Glycine
Glycine is the smallest
residue. It doesn’t have a
side chain, so its
hydrophobicity is a bit
undetermined.
The fact that it doesn’t have a
side chain means that its
backbone is very flexible so
that it can make backbone
turns that other residues
cannot make. It is very bad for
helix, bad for strand, but it is
the star of the turns.
©CMBI 2001
H His Histidine
Histidine is very special. It is a
large hydrophilic residue. Both
its side chain nitrogens can
titrate (the first one at pH 6.2).
It is a little bit aromatic.
It is not particularly picky about
its secondary structure.
It is often seen in active sites. It
is neutral at physiological pH,
but it can easily become
positive, and occasionally even
negative. It can bind metal ions
(mainly Zn, Ni, Cu).
©CMBI 2001
I Ile Isoleucine
Isoleucine is an
intermediately large,
hydrophobic residue.
It is beta branched which
means that it likes to sit in a
strand. It doesn’t mind
sitting in a helix either, but it
cries its eyes out in a turn.
©CMBI 2001
K Lys Lysine
Lysine is a large,
hydrophilic, positively
charged residue.
It is not a good strand
residue, but it doesn’t mind
sitting in a helix or in a turn.
Its side chain is very long
and flexible.
©CMBI 2001
L Leu Leucine
Leucine is an
intermediately large,
hydrophobic residue.
It really loves to sit in a helix.
It is also good for a strand,
but it hates turns.
©CMBI 2001
L Leu Leucine
LEUCINE IS THE MOST ABUNDANT AMINO ACID IN PROTEINS
IN MEMBRANE PROTEINS THE AMOUNT OF LEU IS EVEN HIGHER.
L Leu Leucine
LEUCINE IS CONSIDERED THE "SWITCH" THAT STIMULATES PROTEIN SYNTHESIS.
THE COMBINATION OF WHEY PROTEIN AND ADDED LEUCINE MAXIMIZES MUSCLE
PROTEIN SYNTHESIS BEFORE AND AFTER RESISTANCE EXERCISE.
M Met Methionine
Methionine is a large, sulphur
containing, hydrophobic
residue.
It loves helices, doesn’t
mind sitting in a strand, but
it hates turns.
Methionine can bind metals
with its sulphur, but this sulphur
is not reactive.
It is often the first residue of a
molecule. The N-terminus is
mostly positive and thus mostly
at the surface.
However, very often the Nterminal Methionine is not
present in mature proteins.
©CMBI 2001
M Met Methionine
Methionine is THE Methyl donor in biological processes: S-Adenosyl methionine (SAM)
Methylation is an increasingly interesting topic especially in relationship to DNA
methylation: epigenetics.
However, also during ageing methylation pattern changes - environmental factors.
Age can be calculated from methylation
http://labs.genetics.ucla.edu/horvath/htdocs/dnamage/
Demethylation can occur via TET
enzymes
Michele Zampieri, Fabio Ciccarone, Roberta Calabrese, Claudio Franceschi, Alexander Bürkle, Paola Caiafa
Mechanisms of Ageing and Development, 2015, Available online 20 February 2015
Methionine is necessary and sufficient to increase dietary restriction fecundity.
RC Grandison et al. Nature 000, 1-4 (2009) doi:10.1038/nature08619
http://www.the-aps.org/mm/hp/Audiences/Public-Press/2015-11.html
N Asn Asparagine
Asparagine is an
intermediately large, polar
residue.
It hates the helix, is mildly unamused in a strand, but it
loves the turn.
It can bind metal ions (Ca),
but doesn’t do that as well as
its isosteric partner aspartic
acid.
©CMBI 2001
P Pro Proline
Proline is small and
hydrophobic. In proline, the
side chain is connected to the
backbone at two places: the C
and the N.
Proline does not have a
backbone proton*, and thus is
not good for helices and
strands.
Due to the extra covalent bond,
proline is already ‘pre-bend’, and
thus good for turns. And turns
tend to be at the surface. So,
even though it is very
hydrophobic, Pro often sits at the
surface.
We call this a forced marriage.
*Except at the N-terminus, of course.
©CMBI 2001
P Pro Proline
Bone and skin contain large amounts of proline/hydroxyproline
Bone is a mixture of hydroxylapatite and collagen
Collagen is unusual proline and hydroproline rich protein
https://en.wikipedia.org/wiki/Collagen
Hydroxylapatite is a calcium phosphate molecule
https://en.wikipedia.org/wiki/Hydroxylapatite
Which protein is very rich in calcium, phosphate and proline: Casein!
http://nutritiondata.self.com/foods-000095000000000000000.html
Cows milk is the most casein rich milk source known (much more than human, goat or
sheep). A lot of milk --- relationship to bone and skin development - taller.
But also other sources rich in the components above and contribute as well as individual
differences in gene expression related to proline metabolism.
Q Gln Glutamine
Glutamine is a large,
polar residue.
It is not very picky about its
secondary structure but has
a mild preference for the
helix.
It is isosteric with
glutamic acid.
©CMBI 2001
R Arg Arginine
Arginine is a big,
hydrophilic, positively
charged residue.
It is not picky about
its secondary
structure.
Its side chain contains a socalled guadinium group that
is rigid.
©CMBI 2001
S Ser Serine
Serine is a small,
alcoholic residue of
intermediate
hydrophobicity.
It is not too happy in helices
and strands, but it loves to
sit in turns.
It often forms the active site
of an enzyme together with
histidine and aspartic acid.
It is occasionally involved
in metal (Ca) binding.
©CMBI 2001
T Thr Threonine
Threonine is a small,
alcoholic residue of
intermediate hydrophobicity.
It is beta- branched and
thus good for beta strands.
It doesn’t care about
helices or turns.
It is occasionally involved
in metal (Ca) binding.
©CMBI 2001
V Val Valine
Valine is a small
hydrophobic residue.
It is beta-branched and thus
good for beta strands. Valine
doesn’t care about helices,
but it hates turns.
It is isosteric with threonine.
©CMBI 2001
W Trp Tryptophan
Tryptophan is the biggest
residue. It is aromatic. Despite
that the nitrogen in the five-ring
is donor for hydrogen bonds, it
is very hydrophobic.
It doesn’t care about helices
or turns, but it loves strands.
Size
matters.
Its
size
determines that Trp is the most
conserved of all residues.
©CMBI 2001
Y Tyr Tyrosine
Tyrosine is a large,
aromatic, alcoholic residue
of intermediate
hydrophobicity.
It is not so happy in a helix,
indifferent about turns, and
it loves a strand.
©CMBI 2001