Download Chapter 4 - Evangel University

Mary K. Campbell
Shawn O. Farrell
http://academic.cengage.com/chemistry/campbell
Chapter Four
The Three-Dimensional Structure of Proteins
Paul D. Adams • University of Arkansas
Protein Structure
• Many _________________ are possible for proteins:
• Due to flexibility of amino acids linked by peptide
bonds
• At least one major _________________ has
biological activity, and hence is considered the
protein’s _______________ _________________
Levels of Protein Structure
___ structure: the ________________ of amino acids
in a polypeptide chain, read from the N-terminal end
to the C-terminal end
___ structure: the ______________ ______________
arrangements (conformations) in localized regions of
a polypeptide chain; refers only to interactions of the
peptide backbone e. g., -helix and -pleated sheet
___ structure: 3-D arrangement of all atoms
___ structure: arrangement of monomer subunits with
respect to each other
1˚ Structure
• The 1˚ sequence of proteins determines its 3-D
conformation
• Changes in just one amino acid in sequence can alter
biological function, e.g. hemoglobin associated with
sickle-cell anemia
• Determination of 1˚ sequence is routine biochemistry
lab work (See Ch. 5).
2˚ Structure
• 2˚ of proteins is hydrogen-bonded arrangement of
_________________ of the protein
• Two bonds have _____________ ____________:
1) Bond between _________________ and
_________________ in residue
2) Bond between the _________________ and
_________________ of residue
• See Figure 4.1
-Helix
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Coil of the helix is ___________ or _____________
There are ______ amino acids per turn
Repeat distance is _____ Å
Each peptide bond is _________ and ________
C=O of each peptide bond is _________________
_________ to the N-H of the fourth amino acid away
• C=O----H-N hydrogen bonds are ________________
helical axis
• All R groups point _________________ from helix
-Helix (Cont’d)
-Helix (Cont’d)
• Several factors can _______________ an -helix
• _______ creates a bend because of (1) the restricted
rotation due to its cyclic structure and (2) its -amino
group has no N-H for hydrogen bonding
• strong _________________ _________________
caused by the proximity of several side chains of like
charge, e.g., Lys and Arg or Glu and Asp
• _________________ _________________ caused by
the proximity of bulky side chains, e.g., Val, Ile, Thr
-Pleated Sheet
• Polypeptide chains lie adjacent to one another; may
be _________________ or _________________
• R groups ________, first above, then below _______
• Each peptide bond is ________ and ________
• C=O and N-H groups of each peptide bond are
____________ to axis of the sheet
• C=O---H-N hydrogen bonds are between adjacent
sheets and ____________ to the direction of the
sheet
-Pleated Sheet (Cont’d)
-Pleated Sheet (Cont’d)
-bulge- a common nonrepetive irregular 2˚ motif in
____________ structure
Structures of Reverse Turns
• ____________ found in reverse turns
• Spatial (steric) reasons
• Polypeptide changes direction
• ____________ also encountered in reverse turns. Why?
-Helices and -Sheets
• __________________ structures: the combination
of - and -sections, as for example
•  unit: two parallel strands of -sheet connected by
a stretch of -helix
•  unit: two antiparallel -helices
• -meander: an antiparallel sheet formed by a series of
tight reverse turns connecting stretches of a
polypeptide chain
• Greek key: a repetitive supersecondary structure
formed when an antiparallel sheet doubles back on
itself
• -barrel: created when -sheets are extensive enough
to fold back on themselves
Schematic Diagrams of Supersecondary
Structures
Collagen Triple Helix
• Consists of three polypeptide chains wrapped around
each other in a ropelike twist to form a triple helix
called __________________; MW approx. 300,000
• 30% of amino acids in each chain are Pro and Hyp
(hydroxyproline); hydroxylysine also occurs
• Every third position is Gly and repeating sequences
are X-Pro-Gly and X-Hyp-Gly
• Each polypeptide chain is a helix but not an -helix
• The three strands are held together by hydrogen
bonding involving hydroxyproline and hydroxylysine
• With age, collagen helices become cross linked by
covalent bonds formed between Lys and His residues
Fibrous Proteins
• Fibrous proteins: contain polypeptide chains
organized approximately parallel along a single axis.
They
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consist of long fibers or large sheets
tend to be mechanically strong
are insoluble in water and dilute salt solutions
play important structural roles in nature
• Examples are
• ____________ of hair and wool
• ____________ of connective tissue of animals
including cartilage, bones, teeth, skin, and blood
vessels
Globular Proteins
• Globular proteins: proteins which are folded to a
more or less spherical shape
• they tend to be soluble in ____________ and
____________ solutions
• most of their polar side chains are on the outside and
interact with the aqueous environment by hydrogen
bonding and ion-dipole interactions
• most of their nonpolar side chains are ______ ______
• nearly all have substantial sections of _____________
and ____________
Comparison of Shapes of Fibrous and
Globular Proteins
3˚ Structure
• The ____________ arrangement of atoms in the
molecule.
• In ____________ protein, backbone of protein does
not fall back on itself, it is important aspect of 3˚ not
specified by 2˚ structure.
• In ____________ protein, more information needed.
3k structure allows for the determination of the way
helical and pleated-sheet sections fold back on each
other.
• Interactions between ______ ______ also plays a
role.
Forces in 3˚ Structure
• _________ interactions, including
• _________ _________ between polar side chains,
e.g., Ser and Thr
• _________ interaction between nonpolar side chains,
e.g., Val and Ile
• _________ _________ between side chains of
opposite charge, e.g., Lys and Glu
• _________ _________ between side chains of like
charge, e.g., Lys and Arg, Glu and Asp
• _________ interactions: Disulfide (-S-S-) bonds
between side chains of _________
Forces That Stabilize Protein Structure
3° and 4° Structure
• Tertiary (3°) structure: the arrangement in space of
all atoms in a polypeptide chain
• it is not always possible to draw a clear distinction
between _________ and _________ structure
• Quaternary (4°) structure: the association of
polypeptide chains into _________
• Proteins are divided into two large classes based on
their three-dimensional structure
• _________ proteins
• _________ proteins
Determination of 3° Structure
• X-ray crystallography
• uses a perfect crystal; that is, one in which all
individual protein molecules have the same 3D
structure and orientation
• exposure to a beam of x-rays gives a series of
diffraction patterns
• information on molecular coordinates is extracted by a
mathematical analysis called a Fourier series
• 2-D Nuclear magnetic resonance
• can be done on protein samples in aqueous solution
X-Ray and NMR Data
High resolution method to determine 3˚
structure of proteins (from crystal)
Diffraction pattern produced by electrons
scattering X-rays
Series of patterns taken at different
angles gives structural information
Determines solution structure
Structural info. Gained from
determining distances between
nuclei that aid in structure
determination
Myoglobin
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A single polypeptide chain of ____ amino acids
A single ______ group in a _____________ pocket
8 regions of -helix; no regions of -sheet
Most _______ side chains are on the __________
________ side chains are folded to the __________
Two His side chains are in the interior, involved with
interaction with the heme group
• Fe(II) of heme has 6 coordinates sites; 4 interact with
N atoms of heme, 1 with N of a His side chain, and 1
with either an O2 molecule or an N of the second His
side chain
The Structure of Myoglobin
Oxygen Binding Site of Myoglobin
Denaturation
• Denaturation: the loss of the structural order (2°, 3°, 4°,
or a combination of these) that gives a protein its
biological activity; that is, the loss of biological activity
• Denaturation can be brought about by
• heat
• large changes in pH, which alter charges on side
chains, e.g., -COO- to -COOH or -NH+ to -NH
• detergents such as sodium dodecyl sulfate (SDS)
which disrupt hydrophobic interactions
• urea or guanidine, which disrupt hydrogen bonding
• mercaptoethanol, which reduces disulfide bonds
Denaturation of a Protein
Denaturation and Refolding in
Ribonuclease
Several ways to denature
proteins
• Heat
• pH
• Detergents
• Urea
• Guanadine hydrochloride
Quaternary Structure
• Quaternary (4°) structure: the association of
polypepetide ________ into _____________ proteins
• dimers
• trimers
• tetramers
• Noncovalent interactions
• electrostatics, hydrogen bonds, hydrophobic
Oxygen Binding of Hemoglobin (Hb)
• A _________ of two -chains (141 amino acids each)
and two -chains (153 amino acids each); 22
• Each chain has 1 heme group; hemoglobin can bind
up to 4 molecules of O2
• Binding of O2 exhibited by _________ ___________;
when one O2 is bound, it becomes easier for the next
O2 to bind
• The function of hemoglobin is to transport oxygen
• The structure of oxygenated Hb is different from that
of unoxygenated Hb
• H+, CO2, Cl-, and 2,3-_______________ (BPG) affect
the ability of Hb to _________ & ________ oxygen
Structure of Hemoglobin
Conformation Changes That Accompany Hb Function
• Structural changes occur during binding of small
molecules
• Characteristic of __________________ behavior
• Hb exhibits different 4˚ structure in the bound and
unbound oxygenated forms
• Other _________ are involved in cooperative effect
of Hb can affect protein’s affinity for O2 by altering
structure
Oxy- and Deoxyhemoglobin
Protein Folding Dynamics
• Can 3˚ structure of protein be predicted? Yes, within
limitations
• The integration of biochemistry and computing has led
to bioinformatics
• Protein structure prediction is one of the principal
application of bioinformatics
• First step to predict protein structure is to search for
sequence homology
Predicting Protein Structure
Hydrophobic Interactions
• Hydrophobic interactions are major factors in protein
folding
• Folds so that nonpolar hydrophobic side chains tend
to be on inside away from water, and polar side
chains on outside accessible to aqueous environment
• Hydrophobic interactions are __________________
Hydrophobic and Hydrophilic Interactions in Proteins
Protein Folding Chaperones
• In the protein-dense environment of a cell, proteins
may begin to fold _________ or may associate with
other proteins before folding is completed
• Special proteins called _________ aid in the correct
and timely _________ of many proteins
• hsp70 were the first chaperone proteins discovered
• Chaperones exist in organisms from prokaryotes to
humans