BIO5430/BIO4461 - Macromolecular physical chemistry/Biophysical chemistry

Spring 2004; Notes from the vanHolde, Johnson, and Ho text (D. Gray)
CHAPTER 3 - PART II
3.3.5 Nucleic Acid Structure
The text says that there are 10 variable torsion angels for nucleic acids instead of 2 for
polypeptides. While there are more for nucleic acids than proteins, do you agree that there are
10 torsion angles for a single nucleotide (see Fig. 1.36)? How many for a base pair?
The glycosidic bond torsion angle chi () is at an energy minimum when it is anti and
anti angles are generally favored (Fig. 3.16), except for G in Z-DNA. There is a correlation
between the sugar pucker (see Fig. 1.37) and glycosidic bond torsion angle. We should know
that they are correlated, but skip the 2-D map in Fig. 3.17. Of greater important for nucleic
acid structure are the base pairing, base stacking, and charge repulsion energies.
Base pairing. There are many types of H-bonded base pairs (Fig. 3.18). Generally,
the Watson-Crick base pairs are the most stable, if one considers the pairing of isolated bases.
The book apparently takes the H for forming one H-bond (in CHCl 3) to be about 8 kJ/mol,
and the loss in nucleotide entropy S to be about 47 J/mol at 25C for pairing of two
nucleotides. This means that a G:C pair that forms 3 H-bonds has a favorable G = 3 8 +
14 (which is TS at 25C) 10 kJ/mol. By this calculation, an A:T pair, which has two Hbonds, comes out to be 2 kJ/mol, or the text says about 1 kJ/mol, for the gain due to
base pairing.
Skip the second paragraph on p. 122.
Base stacking. Nucleic acid bases tend to stack (Fig. 3.19). Why? When bases stack,
there is a favorable (negative) enthalpy and an unfavorable (negative) entropy term (Table
3.9). If the stacking interaction is just dipole-dipole and van der Waals interactions, nucleic
acids would not be disrupted by organic solvents (but they are). The idea is, therefore, that the
tendency to stack comes from solvent interactions - i.e. that the bases stack to exclude water.
There are two contributions to the entropy term, one favorable (loss of water so the
hydrophobic bases can interact) and an unfavorable contribution due to the loss of motions in
the nucleic acid strands. The enthalpy term is not only favorable, it is sequence-specific
(Table 3.10). We say that stacking interactions are "nearest-neighbor" interactions. (If you
draw a double-stranded DNA that has 5'-CAGC-3' in one strand and 5'-GCTG-3' in the other,
how many nearest-neighbor stacking interactions would you have? What would the stacking
energy H be, from the values in Table 3.10?)
In general it takes more energy to open a G:C pair in the middle of a double helix than
it takes to open an A:T pair. The nearest-neighbor context is also important. See Table 3.11
for values for RNA. (Calculate from data in Table 3.10 if you predict any difference in the
energy required for opening the central G:C base pair DNA in the middle of CGC/GCG
versus in the middle of AGA/TCT.)
Electrostatic interactions. The negative phosphate charges along the backbone of a
DNA duplex causes the strands to want to repel each other and come apart. The addition of
salt (NaCl) to the solution shields the negative charges and stabilizes the duplex. Charges on
the linear DNA polymer are "screened" by the cations in the solution. Also, some cations

become "condensed" along the DNA. You do not have to struggle with the equations 3.25 or
3.26, but remember that about 76% of the charges along a DNA backbone are compensated
by condensed Na+ over a wide range of salt concentrations. The DNA backbone has a higher
affinity for NH4+ and Mg++ than for Na+.
When basic proteins bind to DNA, the condensed cations are (partially) released.
This, along with release of bound waters, helps favor the binding of proteins to DNA (Table
3.12).
SIMULATING MOLECULAR STRUCTURE
Energy minimization. To find a conformation of lowest potential energy, the force
(from equation 3.3) is calculated for a small change in r. If it is attractive, the coordinates are
changed to the new ones, and the process is repeated. There are several algorithms used for
this calculation. One is called the "steepest descent" method. The minimum that is found is a
local, not necessarily a global, minimum (Fig. 3.21).
Molecular dynamics. We now want to describe the motion of a molecule, not just its
static energy (potential energy). In essence, the motion of each atom is related to its kinetic
and potential energies (by Eqn. 3.28). K depends on the temperature. If the total energy is
constant, the higher the temperature the more the energy is partitioned into kinetic energy. For
molecular dynamics, we define a temperature and a time interval t. The velocity distribution
is determined by the temperature (Fig. 3.22). Some limitations are that the temperature often
has to be high, to compensate for rigid bonds, and the time interval has to be short for an
accurate calculation.
One use of molecular dynamics is simulated annealing, to allow the molecule to find a
more global energy minimum (Fig. 3.23).
Entropy. How do we take the entropy, not just the enthalpy, into account in
determining the conformation of a macromolecule? If there are 9 allowed combinations of
and for each of n1 linkages between n amino acids, we have N = g^(n1) = 9^99 for the
number of conformations of a 100-residue polypeptide. The difference in entropy between the
native structure and all possible structures is
S = kB (ln(1) lnN) = kB (1n) ln(g). Or, per mole S = R(1n) ln(g). (Confirm that
this does give about 2 kJ/(mol K) for a 100 residue polypeptide.)
Eqn 3.33 should have a minus sign, and the n2 should be n1.
A problem is that the number of possible conformations is so large that they could not
all possibly be sampled in the course of folding into the correct one. Protein folding typically
occurs through a restricted number of states, via "molten globule" intermediates that are
partially folded, and is helped by chaperones and other enzymes.
We will skip the remaining topics in Chap. 3 from p. 135-144.