ULTIMATE COMPUTING - Quantum Consciousness Studies

130 Protein Conformational Dynamics
required to include one example of each of this number of protein structures
would far exceed that of the universe!
Amino acids which comprise polypeptide chains and primary protein
structure can form linkages with other amino acids within the polypeptide by
hydrogen bonds and disulfide bonds. These linkages cause bending of polypeptide
chains into coiled or folded structures which determine protein secondary
structure. The most stable and commonly observed secondary structure is a right
handed coil called an “alpha helix” in which hydrogen bonds (Figure 6.1) form
between an oxygen and a hydrogen separated by 3 or 4 amino acids on the
polypeptide chain. Alpha helices can interact among themselves in a protein,
stacking in parallel or antiparallel arrangements or forming left handed “coiledcoils.”
Alpha helices (Figure 6.2) are common occurrences in a wide variety of
proteins; tubulin is about 40 percent alpha helix in most circumstances (Dustin,
1978). The alpha helix has been proposed as an important site of energy and
information transfer in proteins. Davydov has proposed that the energy of ATP
hydrolysis utilized in actin-myosin muscle contraction and many other biological
events is conveyed along alpha helix pathways via propagating “solitons” which
occur due to enharmonic coupling in the carbon-oxygen double bonds (Section
6.7).
Hydrogen bonds forming among amino acid-side groups on polypeptide
chains in parallel result in planar secondary protein configurations called betapleated
sheets. First proposed by Linus Pauling in 1951, beta pleated sheets may
themselves align in parallel, antiparallel or mixed formations.
Alpha helices, beta pleated sheets and other secondary structures interact to
define protein tertiary structure, upon which most protein functions depend.
Hydrophobic forces, charge distribution, disulfide bridges and secondary structure
result in folding into globular regions which define the shape of single protein
units. Alpha helix and beta pleated sheets pack into arrangements which help
determine the tertiary structural domains which often have specific functions like
binding a molecule, or associating with other domains to create larger structures.
Assembly of groups of tertiary structure determines quaternary structure, like
tubulin subunits assembling into microtubules. Generally, hydrophobic
interactions like Van der Waals forces are important in quaternary protein
assemblies.
Levels of protein assemblies include, at the simplest level, monomeric
enzymes. Weighing from 20 to 90 kilodaltons, these enzymes have a single active
site at which specific molecules undergo chemical reactions facilitated
(“catalyzed”) by the enzyme. Some enzymes may require metal ions, organic
molecules or specific cofactors to function. Reduced enzymatic activity can result
from occupancy of the active site by molecules resistant to enzymatic action, a
phenomenon called “competitive inhibition.” Active site binding corresponds
with specific conformational states of enzymes.
A more complex system is the oligomeric enzyme, an example of which is the
acetylcholine receptor: a four subunit oligomer which is activated by binding of
acetylcholine. Being composed of several subunits leads to collective properties
which arise from the organization and interactions of the components. Many or
perhaps most enzymes are oligomeric with molecular weights ranging from 35 to
several thousand kilodaltons. Oligomeric subunits often have two binding sites;
one is the active site for its enzyme action and the other is a regulatory site which
controls the active site by a change in subunit shape or conformation. Regulatory,
or effector molecules can change not only the catalytic site activity on that subunit
(allosterism) but also on adjacent subunits (cooperativity). Oligomer subunits may
be alike (homopolymers) or different (heteropolymers) and coenzymes may be