The 3Dimensional Structure of Proteins

1
Chapter 4

• The 3-Dimensional Structure of Proteins

2
Objectives

• What forces drive the folding of proteins?
• Describe the levels of protein structure.
• What are the constraints and determinants of
  adopting various structures?
• What are some examples of proteins that display
  various structural motifs?

3

• Three-dimensional, functional structure is called
  native
• Folded shape is called conformation
• There are thousands of possible conformations,
  but not an infinite amount
• Conformations are restrained by
• planarity of peptide bond
• allowed angles

4
The 4 levels of protein stucture

• Primary Linear amino acid sequence
• Bonds Covalent
• Secondary Local structure certain motifs are
  common
• Bonds Mostly H-bonds
• Tertiary Complete 3-D shape
• Bonds H-bonds, hydrophobic interactions, ionic
  bonds, van der Waals interactions, disulfide
  bonds
• Quaternary gt1 peptide chains
• Bonds Mostly H-bonds

5
(No Transcript)
6
There is no free rotation about the peptide bond
due to resonance. This limits the number of
possible conformations.
7
Psi (?) Dihedral angle between C? and
Ccarbonyl Phi (?) Dihedral angle between N and
C?
Ramachandran Plot
8
Ramachandran Plot for L-Ala
9
Secondary Structure

• The alpha helix
• Tightly wound, repeating sequence
• Right-handed
• R-groups are on outside of helix
• Each twist ? 5.4 Å 3.6 residues
• Stabilized by H-bonds between N-H and CO 3
  residues away
• a-helices are polar (positive at amino end
  negative at carboxyl)
• Some amino acids are a-helix breakers
• Repeating like-charges
• Repeating bulky groups

10
(No Transcript)
11
(No Transcript)
12
Alpha Helix, continued

• Effects on helical stability
• Electrostatic interactions between adjacent
  residues
• Steric interference between adjacent residues
• Interactions between residues 3-4 amino acids
  away
• Pro and Gly (helix breakers)
• Polarity of residues at both ends of helix

13
(No Transcript)
14
Beta Conformation

• Extended, zigzag conformation
• Interactions between adjacent amino acids
• Adjacent strands, H-bonded to one another, lead
  to beta sheet
• R-groups protrude opposite of parallel structure

15
Beta Sheet

• Parallel ?-sheet
• Same Amino-carboxyl direction
• (6.5 Å repeat)
• Anti-parallel ?-sheet
• Opposite orientation
• (7 Å repeat)

16
(No Transcript)
17
?-turns

• Interacting strands can be many amino acids apart
• Turns are 180 connect strands in folded
  (globular) proteins
• Interaction is between carbonyl oxygen of aa 1
  and amino hydrogen of aa 4
• Interior amino acids are not involved thus, Pro
  and Gly are often present (Type II turns)
• Gly small and flexible
• Pro Cis conformation makes inclusion in tight
  turn favorable

18
Proline isomerization
19
?-turns, continued

• Type I (most common) Type II ALWAYS contain Gly
  as amino acid 3.

20
Bond angles (?, ?) describe secondary structure
21
(No Transcript)
22
Tertiary Structure

• Long range protein structure
• Interactions between various secondary structural
  components of protein
• 2 major classifications
• Fibrous (structural proteins) vs. globular

23
Fibrous Proteins

• Strong and flexible
• Hydrophobic
• Comprise hair, quills, wool, nails, etc.
• Left-handed helix of intertwined a-helices (of
  smaller repeat period) confer strength this
  forms super-structure called protofilaments,
  which combine to form fibrils

24
Alpha-keratin
25
CollagenLeft-handed helix 3 aa/turn
26
Collagen

• Tightly wound left-handed helix
• Gly-X-Y
• X Pro Y 4-Hyp

Hydroxyproline requires Vitamin C for proline
hydroxylationScurvy?
27
Globular Proteins

• Water-soluble
• Examples
• Enzymes (Hexokinase)
• Transport proteins (Myoglobin)
• Immune system proteins (Antibodies)
• More to come on this in subsequent lectures

28
(No Transcript)
29
Protein Domains
Troponin C
30
Domains
31
(No Transcript)
32
(No Transcript)
33
(No Transcript)
34
Levinthals Paradox

• For random protein folding, make several
  assumptions
• Since there are 2 torsional angles (?, ?), assume
  3 stable values for each
• Assume protein of n amino acids
• There are then 32n ? 10n possible conformations
• 1013 conformations can be tested per second (time
  for single bonds to re-orient)
• the time for all possible conformations is given
  by
• t 10n/1013 and, for a protein of 100 amino
  acids, t 1087 s 1079 years!!!

35
Thermodynamics of protein folding
Greater stability
36
Molten Globule

• An intermediate state in the folding of protein
  pathway of a protein that has some secondary and
  tertiary structure, but lacks the well packed
  amino acid side chains that characterize the
  native state of a protein.
• Observed for many protein under both equilibrium
  and non-equilibrium conditions.
• By contrast, for fast folding proteins without
  intermediates, the search for a core or nucleus
  is likely to be the rate-determine step once the
  core is formed, folding to the native state is
  fast

http//zcam.tsinghua.edu.cn/shipl/protein01.ppt2
70,12,Molten Globule