38 BIOCHEMISTRY FUNDAMENTALS
bacterial infection by breaking the tough skin of carbohydrate chains, inter-
locked by short peptide strands, that form the protective cell walls of bacteria.
The lysozyme action destroys the structural integrity of the bacterial cell,
causing it to burst under its own internal pressure. The particular lysozyme
modeled here is a synthetic construct that features a primary sequence of 129
amino acid residues. The X - ray crystallographic data visualized in Figure 2.10
was taken from the protein data bank (PDB) at http://www.rcsb.org/pdb/
home/home.do. Searching the term “ lysozyme ” in this website yielded 991
deposited lysozyme structures in late 2006. The lysozyme structure chosen for
visualization, with PDB accession number 2C8O, dates from 2006.^4 A possible
confusion in entering letters versus numbers when using the PDB should be
explained. The lysozyme PDB: 2C8O data are accessed with the last digit given
as the letter “ O ”. If one enters the number 0 (zero) instead — 2C80 — a different
data set for a different molecule is accessed. The visualization for PDB: 2C8O
was carried out using CambridgeSoft ’ s Chem3D Ultra Version 10.0 software,
saved as a .png fi le in Chem3D, then opened with ChemDraw Ultra Version
10.0 for additional notations. (See Chapter 4 for more information on Cam-
bridgeSoft software.)
Figure 2.10 visualizes the compact, globular, 129 - amino - acid residue lyso-
zyme protein that exhibitsα - helical, β - pleated sheet, random coil and connect-
ing loop secondary structure. Seven α - helices, some of them distorted and
some short, can be identifi ed: (1) residue arg5 – arg14, contains cys6; (2) tyr20 –
gly22; (3) leu25 – ser36, contains cys30; (4) cys80 – leu84, contains cys80; (5)
thr89 – val99, contains cys94; (6) gly104 – arg114; and (7) val120 – ile124. Three
antiparallelβ - pleated sheet segments are also identifi ed. The protein is knitted
together into its tertiary, globular structure by four disulfi de bonds between
the eight cysteine residues found in lysozyme. The bonds are formed between
(1) cys6 (in helix 1) near the protein ’ s N - terminal end and cys127 (in random
coil) near the C - terminal end; (2) cys30 (in helix 3) and cys115 (in random coil
connecting distorted helices 6 and 7); (3) cys76 (in a long loop connecting the
fi nal segment of the β - pleated sheet with helix 4) and cys94 (in helix 5); and
(4) cys64 (also found in the long loop connecting the fi nal segment of the β -
pleated sheet with helix 4) and cys80 (the fi rst residue in helix 4).^5
Most proteins contain more than one polypeptide chain. The manner in
which these chains associate determines quaternary structure. Binding involves
the same types of noncovalent forces mentioned for tertiary structure: van der
Waals forces, hydrophobic and hydrophilic attractions, and hydrogen bonding.
However, the interactions are now interchain rather than intrachain (tertiary
structure determination). The quaternary structure of hemoglobin (four almost
identical subunits) will be discussed in Section 7.2.
Secondary structure, as well as tertiary and quaternary structure of proteins,
is intimately dependent on the primary sequence of amino acids in the chain.
In fact, the manner in which proteins fold into their ultimate structures in
biological species is a subject of much research and continued uncertainty even