Transcript Tertiary Structure

Motifs of Protein Structures
Branden & Tooze, Chapter 2
Central Dogma of Molecular Biology
protein
Translation
in ribosome
DNA
Transcription
RNA
Protein Sequence to Structure
1°
4°
2°
3°
The primary structure is the sequence of AAs. Once formed, the sequences form
secondary and tertiary structures, and sometimes quaternary structures, that are
critical to their functions.
Proteins 1° Structure: The Sequence of Amino
Acids
• Primary (1°): Sequence of amino acids
– Primary structure held together by peptide bonds
– Protein sequence determined by sequence of a gene in the
genetic code
– Determines 3D structure
http://protein-pdb.com/2011/10/04/primary-protein-structure/
Protein 2° Structure
Seager SL, Slabaugh MR, Chemistry for Today: General, Organic and Biochemistry, 7 th Edition, 2011
Protein 2° Structure: The α-helix
• In globular proteins, may vary in length from 4-40 residues
• AA’s in an α helix arranged in a right-handed helix
• Each amino acid residue is rotated 100° relative to previous residue
in helix
– Helix has 3.6 residues per turn
– H-bonds form between N-H groups at residue n and C=O groups at n+4
http://simplygeology.wordpress.com/tag/s-waves/
Helices – 3 Major Types
http://www.cryst.bbk.ac.uk/PPS2/course/section8/ss-960531_5.html
310 Helix
• 3 residues per turn and 10 atoms between Hbond donor and acceptor (n to n+3)
• Occurs rarely, and usually at end of α helix or as
single turn helix
• Not energetically favorable since backbone
atoms packed too tightly
π Helix
• H-bonding occurs between residues n to n+5
• Occurs rarely, and usually at end of α helix or as
single turn helix
• Not energetically favorable since backbone
atoms packed too loosely (hole in the middle)
α Helix has dipole moment
• All N-H to C=O H-bonds go in the same direction, so there is a
net pull of electron density towards the C-terminal end of the
helix.
• Negatively charged ligands (e.g., phosphate groups) may bind
to positively-charged N-terminal end, but the reverse is less
likely to be observed.
δ+
δ-
N-terminal
C-terminal
Protein 2° Structure: α Helices
• Some residues more likely to be in helices than others:
• Good helix formers: Met (M), Glu (E), Ala (A), Leu (L)
• Poor helix formers: Gly (G), Pro (P), Ser (S), Tyr (Y)
• Helices tend to be on outside of protein, or have polar ends on the outside
(hydrophilicity)
• Side chains tend to change from hydrophobic to hydrophilic every 3-4
residues
• Hydrophobic and hydrophilic residues tend to aggregate on opposite sides of
the helix (see helical wheel below).
Proteins 2° Structure: The β-sheet
• Beta (β) sheets (or pleated sheets) formed by H-bond connected
strands
• β strands are like elongated helices without helical H-bonds
– Usually 5-10 residues long
• β Sheets may be parallel or antiparallel
http://www.chembio.uoguelph.ca/educmat/phy456/456lec01.htm
Proteins 2° Structure: Random Coils and Loops
• Proteins typically contain regions lacking either sheet or helical
structures.
– These are called Random Coils or Loops
– Usually found at surface of protein (with charged and/or polar residues)
• Loops may perform important structural and functional roles,
including:
– Connecting β strands form antiparallel sheets (hairpin loops or reverse turns)
– Increasing flexibility (hinge motion)
– Binding metal ions or other biomolecules to alter protein function
http://www.chembio.uoguelph.ca/educmat/phy456/456lec01.htm
Proteins 3° Structure
• Protein function determined by 3D shape
• Tertiary structure results from residue interactions:
–
–
–
–
H-bonding
Disulfide Bridges
Salt Bridges
Hydrophobic Interactions
Seager SL, Slabaugh MR, Chemistry for Today: General, Organic and Biochemistry, 7 th Edition, 2011
Proteins 3° Structure
• Polar and charged residues tend to be on surface of protein, exposed
to water, while hydrophobic residues tend to be buried
Seager SL, Slabaugh MR, Chemistry for Today: General, Organic and Biochemistry, 7 th Edition, 2011
Proteins 4° Structure
• Functional proteins may
contain two or more
polypeptide chains held
together by the same forces
that control 3° structure:
–
–
–
–
H-bonding
Disulfide Bridges
Salt Bridges
Hydrophobic Interactions
• Each chain is a subunit of
structure
• Each subunit has its own 1°,
2° and 3° structure
Seager SL, Slabaugh MR, Chemistry for Today: General, Organic and Biochemistry, 7 th Edition, 2011
John Kendrew, 1958,
upon determining the molecular
structure of myoglobin:
“Perhaps the most remarkable features of the
molecule are its complexity and
its lack of symmetry.
The arrangement seems to be almost totally
lacking in the kind of regularities which one
instinctively anticipates,
and it is more complicated than has been
predicted by any theory of protein structure.”
Tertiary Structure
Tertiary structure describes how the secondary
structure units associate within a single
polypeptide chain to give a three-dimensional
structure.
Tertiary structures can be divided
into three main classes:
a domain
b domains
a/b domains
Quaternary structure describes how two
or more polypeptide chains associate to
form a native protein structure (but some
proteins consist of a single chain).
Proteins are Large Macromolecules
• Proteins are extremely large
– MW of glucose is 180 u, compared with 65,000 u for hemoglobin
• Proteins synthesized inside cells remain inside cells
– The presence of intracellular proteins in blood or urine can be used to test for certain
diseases
Seager SL, Slabaugh MR, Chemistry for Today: General, Organic and Biochemistry, 7 th Edition, 2011
Protein Functions
• Catalytic Function:
– Enzymes are proteins that catalyze biological functions
• Structural function:
– Most human structural materials (excluding bone) are comprised of proteins
– Collagen (bundled helices)
• 25-35% of total protein in body
• Tendons
• ligaments
• Skin
• Cornea
• Cartilage
• Bone
• blood vessels
• gut
– Keratin (bundled helices)
• Chief constituent of hair, skin, fingernails
http://www.imb-jena.de/~rake/Bioinformatics_WEB/proteins_classification.html
Protein Functions
• Storage Function:
– Storage of small molecules or ions
– Ovalbumin
• Main protein in egg whites
• Can be broken down into amino acids for use by developing embryos
– Ferritin
• Globular complex of 24 protein subunits
• Buffers iron concentration in cells
Ovalbumin (chicken egg white)
http://www.stagleys.demon.co.uk/explorers/genesandproteins/page6.html; http://ferritin.blogspot.com/
ferritin
Protein Functions
• Protective Function:
– Protection against external foreign
substances
Immunoglobulin
• Antibodies
– Very large proteins
– Combine with, and destroy viruses, bacteria
– blood clotting/Coagulation
• thrombin
– Protease responsible for platelet aggregation
and formation of fibrin
Harris, L. J., Larson, S. B., Hasel, K. W., Day, J., Greenwood, A., McPherson, A. Nature 1992, 360, 369-372; http://courses.washington.edu/conj/immune/antibody.htm;
http://www.colorado.edu/intphys/Class/IPHY3430-200/014blood.htm
Protein Functions
• Regulatory Function:
– Protein hormones
• Insulin
– Protein hormone that directs cells in the liver,
muscle, and fat to take up glucose from the blood
and store it as glycogen
– Forms hexamer bound together by Zn
Insulin
http://en.wikipedia.org/wiki/File:InsulinHexamer.jpg; Seager SL, Slabaugh MR, Chemistry for Today: General, Organic and Biochemistry, 7 th Edition, 2011
Protein Functions
• Nerve impulse transmission:
– Rhodopsin
• Protein found in rods cells of eye retina
– Converts light events into nerve impulses sent to
the brain
http://cherfan2010biology12assessment.wikispaces.com/The+Retina
Protein Functions
• Movement function:
– Proteins involved in muscle contraction
• Myosin
• Actin
http://www.sigmaaldrich.com/life-science/metabolomics/enzyme-explorer/learning-center/structural-proteins/actin.html
Protein Functions
• Transport function:
– Transport ions or molecules throughout the body
• Serum albumin: Transports fatty acids between fat and other tissues
• Hemoglobin: Transports O2 from lungs to other tissues (e.g., muscles)
• Transferrin: Transports iron in blood plasma
Serum albumin
hemoglobin
transferrin
http://en.wikipedia.org/ ; http://www.pdb.org/pdb/101/motm.do?momID=37
Many Proteins Contain Intrinsic Metal Atoms
• (a) The di-iron center of the
enzyme ribonucleotide
reductase. Two iron atoms
form a redox center that
produces a free radical in a
nearby tyrosine side chain.
The coordination of the iron
atoms is completed by
histidine, aspartic acid, and
glutamic acid side chains as
well as water molecules.
• (b) The catalytically active
zinc atom in the enzyme
alcohol dehydrogenase.
The zinc atom is
coordinated to the protein
by one histidine and two
cysteine side chains.
Calcium-binding proteins (CaBPs)
Binding affinities
Triggering
Buffering
Kd (M)
10-3CaR
Ca
10-4
Thermolysin
10-5
Calmodulin
10-7
Protease K
Ca2+-free Calmodulin
(1cfc)
Stabilizing
Ca2+-binding Calmodulin
(3cln)
Calbindin D9K
(1b1g)
Assembly/Folding
10-8
Calbindin D9k
10-9
α-Lactalbumin
Parvalbumin
Thermolysin (1tlx)
Cocksfoot mottle virus capsid (1ng0)
Protein Classifications
Based on structural shape
• Fibrous Proteins
– Comprised of long stringlike molecules that can wrap around each other to form fibers
– Usually insoluble in water
– Major components of connective tissues (e.g., collagen, keratin)
• Globular proteins
– Spherical
– Usually water soluble
– May be moved through the body (e.g., hemoglobin, transferrin)
Based on composition
• Simple Proteins
– Contain only amino acid residues
• Conjugated Proteins
– Contain amino acid residues and other organic or inorganic components (i.e., prosthetic
groups)
• Lipoproteins
• Glycoproteins
• metalloproteins
http://www.sigmaaldrich.com/life-science/metabolomics/enzyme-explorer/learning-center/structural-proteins/actin.html
Folds of Proteins
Helix,
strand
Motifs
Folds/
Domain
Domains
Super Secondary Structures (Motifs)
• Simple combinations of a few secondary structural
elements with a specific geometric arrangement are called
super secondary structures or motifs.
• They may have functional and structural significance.
• Individual motifs may not be stable folding units. They may
require association with other motifs.
• Common motifs:
Helix-turn-helix
b-hairpin, b-meander
b-barrel, Geek key
bab
Helix-Turn-Helix Motif
• Two a helices that are connected by a short loop
region in a specific geometric arrangement constitute a
helix-turn-helix motif. (a) the DNA-binding motif and (b)
the calcium-binding motif, which are present in many
proteins whose function is regulated by calcium.
EF-hand Calcium-binding Motif
• The calcium atom is bound to one of the motifs in the
muscle protein troponin-C through six oxygen atoms:
one each from the side chains of Asp (D) 9, Asn (N) 11,
and Asp (D) 13; one from the main chain of residue 15;
and two from the side chain of Glu (E) 20. In addition, a
water molecule (W) is bound to the calcium atom.
Amino Acid Sequences of EF-hand
Motifs
1
3
5
7
9
12
• The side chains of hydrophobic residues on the flanking helices form a
hydrophobic core between the a helices
• From the sequences above, it can be seen that some residues or types of
residues are highly conserved between motifs.
Beta Sheet Topology Diagrams
transcarbamoylase
flavodoxin
plastocyanin
• Beta sheets are usually represented simply by arrows in
topology diagrams that show both the direction of each b
strand and the way the strands are connected to each other
along the polypeptide chain.
The b Hairpin Motif
Bovine Trypsin Inhibitor
Snake Venom Erabutoxin
• The hairpin motif is very frequent in b sheets and is built up from two
adjacent b strands that are joined by a loop region.
• For 2 sequentially adjacent hairpin motifs, they can be arranged in 24
different arrangements (conformations)
Greek Key Motif
The Greek key motif is found in antiparallel b sheets when
four adjacent b strands are arranged in the pattern shown
as a topology diagram in (a). The three dimensional
structure of the enzyme Staphylococcus Nuclease shown
in (b) in blue and red is also a Greek key motif.
Forming Greek Key Motif
• Suggested folding pathway
from a hairpin-like structure
to the Greek key motif.
• Beta strands 2 and 3 fold
over such that strand 2 is
aligned adjacent and
antiparallel to strand 1.
b-a-b Motif
• Two adjacent parallel b strands are usually
connected by an a helix from the C-terminus of
strand 1 to the N-terminus of strand 2.
• Most protein structures that contain parallel b
sheets are built up from combinations of such b-ab motifs.
b-a-b Handedness
• The b-a-b motif can in principle have two "hands."
• (a) This connection with the helix above the sheet is
found in almost all proteins and is called right-handed
because it has the same hand as a right-handed a
helix.
• (b) The left-handed connection with the helix below
the sheet.
Adjacent Motifs
Motifs that are adjacent in
the amino acid
sequence are also
usually adjacent in the
three-dimensional
structure.
Triose-phosphate
isomerase is built up
from four b-a-b-a
motifs that are
consecutive both in the
amino acid sequence
(a) and in the three
dimensional structure
(b).
Domains
• "Within a single subunit [polypeptide chain], contiguous
portions of the polypeptide chain frequently fold into
compact, local semi-independent units called domains." Richardson, 1981
• Domains may be considered to be connected units, which
are to varying extents independent in terms of their
structure, function and folding behavior.
• Each domain can be described by its fold. While some
proteins consist of a single domain, others consist of
several or many. A number of globular protein chains
consist of two or three domains appearing as 'lobes'.
• In other cases, the domains may be of a very different
nature. For example, some proteins located in cell
membranes have a globular intracellular or extracellular
domain distinct from that which spans the membrane.
Domain Organization
• Small protein molecules like the epidermal growth factor,
EGF, are comprised of only one domain. Others, like the
serine proteinase chymotrypsin, are arranged in two
domains that are required to form a functional unit. Many of
the proteins that are involved in blood coagulation and
fibrinolysis have long polypeptide chains that comprise
different combinations of domains.
Mosaic Proteins
• Mosaic proteins are those which consist of many repeated
copies of one or a few domains, all within one polypeptide
chain.
• Many extracellular proteins are of this nature. The domains
in question are termed modules and are sometimes
relatively small. Note that this term is often applied to
sequences whose structures may not be known for certain.
Myosin