1. Introduction to Biophysics Lecture 5 Proteins Structure

2. Proteins
hemoglobin

3. Isomers: Biological molecules consist of: C, H, O, N, P
isomers are compounds with the same molecular formula but different structures
A simple example of isomerism is given by propanol: C3H8O (or C3H7OH)
propan-1-ol (n-propyl alcohol; I), propan-2-ol (isopropyl alcohol; II) and methoxyethane III

4. Isomers: Chiral Chain isomerism Position isomerism
Functional group isomerism
Chiral

5. Rotamers: Energy, a.u. Dihedral angle
The conformational state shows how atoms are arranged in space. The conformational state of a molecule has a profound impact on what it does, and much of the work in molecular biophysics deals with understanding molecular conformations, both what they are and how they perform biological functions.

6. Enantiomers:

7. Isomers:
D and L. L-amino acids represent the vast majority of amino acids found in proteins, while D-amino acids are found in some proteins produced by exotic sea-dwelling organisms, such as cone snails. They are also abundant components of the peptidoglycan cell walls of bacteria.
(The L and D convention for amino acid configuration refers not to the optical activity of the amino acid itself, but rather to the optical activity of the isomer of glyceraldehyde from which that amino acid can theoretically be synthesized (D-glyceraldehyde is dextrorotary; L-glyceraldehyde is levorotary). )

9. This reaction can occur through the energy-driven action of the ribosome. Ribosomes are complexes of proteins and RNA that translate a gene sequence in the form of mRNA into a protein sequence.
How difficult is to destroy peptide bond?

10. Ribosome – molecular machine that synthetizes proteins

12. Peptide bond
These bond lengths and angles reflect the distribution of electrons between
atoms due to differences in polarity of the atoms, and the hybridization of their
bonding orbitals.

13. Double bond:
sp2

14. Like any double bond, rotation about the peptide bond angle  is restricted, with an energy barrier of ˜3 kcal/mole between cis and trans forms. These two isomers are defined by the path of the polypeptide chain across the bond.
For all amino acids but proline, the cis configuration is greatly disfavored because of steric hindrance between adjacent side chains.

15. While there is restricted rotation about the peptide bond, there is free rotation about the four bonds to the a-carbon of each residue. Two of these rotations are of particular relevance for the structure of the polypeptide backbone. To fully appreciate these rotations, we must shift our perspective from the peptide-bond centered view to the C-centered view.

16. Ramachandran plots (1963)
limiting called hard-sphere boundary (atoms clash)
Glycine
R = H R
For -branched residues the restrictions are severe, and only a small fraction of , space is allowed.
-strand
Two common regular secondary structures that can be adopted by the polypeptide backbone, the -helix and -strand. There is an energy barrier between -helix and -strand regions.
-helix

17. Can we predict secondary structure from primary structure?
There is no sequence dependence on the steric restrictions of the  and  space because , restrictions arise within each residue rather than between residues.
However, a sequence of residues that all have similar allowed , space can give rise to a chain segment that forms  or  structures.

18. -helix looks like spring
H-bonds
dipoles
The side chains project outward
The most common shape is a right handed -helix defined by the repeat length of 3.6 amino acid residues and a rise of 5.4 Å per turn. Thus residues (i+3) and (i+4) are closest to residue (i) in the helix.

19. -strands: parallel or antiparallel
-helix
The side chains project alternately up and down

20. hairpin
Linearly distant residues are brought into proximity at the N-and C- terminal ends of the hairpin.

21. Hydrophobic interactions
Often – tightly packed core of hydrophobic residues
protein secondary and tertiary structures are lost concomitantly and in an all-or none
manner upon changes in environment that disfavor the folded state, such as
higher temperature or solvent additives.

22. Denaturation
Denaturation is the unfolding of the protein from rigid, regular arrangement to the irregular, diffuse arrangement of the flexible open chain (molten globe).
G 50 kJ/mol.
pH, T, ionic conditions, solvent

23. Thinking again about folding:
Protein with 300 amino acids, each of which could have 8 rotational positions
8300=10270
-helix, -strand arrangements limit number of possible configurations
Chaperons – reversibly bind to specific sequence in primary structure and help to avoid wrong ways of folding.
Poly-cis/trans-isomerases – directly promotes process of folding. Peptide bonds are synthesized in trans configuration but 7% occur in cis due to isomerases activity.

24. Approximation to total potential energy of the protein
U =
bonds a(xi-xi,0) (stretching energy of all covalent bonds, a force constant)
+bond angles b(i -i,0) (bending energy of all bonds)
+dihedral angles c(1 – cos(n i(i -i,0))) (rotational potential of dihedral angles)
+charges qiqj/(r)rij (electrostatic interaction)
+neutral atoms 4d((rij0/rij)12 – (rij0/rij)6) (Lennard-Jones potential)
Computer time needed to find the true minimum increases exponentially with the size of the molecule.
Each term has limited accuracy. (101 kcal/mol)
Total energy is a sum of thousands of such terms (N). (N=10,000)
Error of the sum = average error per term * N (U=100,000100 kcal/mol)

25. Prof. David Baker developed a protein folding game:
Critical Assessment of protein Structure Prediction, or CASP, is a community-wide, worldwide experiment for protein structure prediction taking place every two years since 1994

26. Conformational states of proteins are the basic building blocks in
mechanistic models, and interconversions between these states are the
basic molecular signaling events.
Examples
the activation of membrane receptors,
the regulation of gene expression,
the control of cell division,
the gating of ion channels,
and the generation of mechanical force.

27. Protein Data Bank
Home work:
Download “pdf” file of Lysozyme (from bacteriophage) from Protein Data Bank
Download and install VMD Illinois software
Generate Ramachandran plot for Lysozyme
Download Swiss PDB viewer
Analyze interaction of threonine 157 with other aminoacids.
Identify H-bonds between Thr –OH group and other residues. List names of interacting residues and H-bond distances to them (heavy atom to heavy atom).

28. Reading:
Nelson, Chapter 2