Protein Folding with the Parallel Replica Exchange Molecular Dynamics Method - Parallel Computing for Bioinformatics and Computational Biology - page 408

Figure 17.5 Water coordination to the backbone carbonyl oxygen atoms along the peptide
sequence. The coordination number is about 1, except when the carbonyl group is four amino
acids before an Arg side chain. The Arg side chain shields the carbonyl oxygen atom from
exposure to water.

17.3.4 Folding of a β -Hairpin

The second example, the C-terminus β -hairpin of protein G, has recently received
much attention from both experimental and theoretical fronts [38-47]. Its fast folding
speed (folds in 6 s) and reasonable stability in aqueous solution make it a system

of choice for studying the β -hairpin folding in isolation. Again, we use the highly
parallel REMD to study the free energy landscape and folding mechanism of this
β -hairpin.
The free energy landscape is often calculated by the histogramming analysis
[44, 48]

µ

1
Z exp (

P(X) = − βW(X)) (17.16)

and

kT log P(X 2 )
P(X 1 )

,

W(X 2 ) − W(X 1 ) =− (17.17)

where P(X) is the normalized probability obtained from a histogram analysis as a
function of X . X is any set of reaction coordinates (RCs) or any parameters describing
the conformational space. W(X 2 )

W(X 1 ) is thus the relative free energy or so-called
potential of mean force (PMF). Here, we will use the number of β -strand hydrogen
bonds ( N β

−

HB ) and the radius of gyration of the hydrophobic core ( R cor g ) as the RC
for the free energy contour map (many other RCs have also been used [15]). N β

HB is
defined as the number of native β -strand backbone hydrogen bonds excluding the two