ULTIMATE COMPUTING - Quantum Consciousness Studies

Protein Conformational Dynamics 129
6 Protein Conformational Dynamics
Proteins are the structural and organizational elements of “the living state.”
Their essential functions are intrinsically linked to their structure and dynamic
switching among different conformational states. For example, ion channel
proteins embedded in a membrane may be either in an “open” conformation,
through which specific ions diffuse along a gradient, or they may be “closed.”
This type of conformational switch does not require biochemical energy such as
ATP hydrolysis, but utilizes energy stored in transmembrane voltage gradients
and occurs in response to an appropriate trigger. Proteins such as enzymes,
receptors, cytoskeletal filaments, muscle myosin and hemoglobin undergo
important conformational changes in response to a variety of stimuli. Dynamic
patterns of conformational states among cytoskeletal subunits may represent
information, exert control over routine biological functions, and provide the
“grain of the engram.”
6.1 Protein Structure
Figure 6.1: Hydrogen bond between hydrogen and oxygen in amide one
resonance bond. With permission from Bolterauer, Henkel and Opper (1986).
Proteins have several hierarchical levels of structural organization which
determine their dynamic and functional capabilities. Protein primary structure is
determined by a sequence of 22 possible amino acids held together by peptide
bonds. An amino acid consists of carbon atoms bound to nitrogen atoms (peptide
bond) and their attendant side groups. The 22 amino acids found in proteins differ
in their side groups although each contains a carbon-oxygen double bond known
as “amide 1.” Strings of amino acids called “peptides” perform many
physiological functions including acting as neurotransmitters and circulating
hormones. The amino acids impart specific properties according to the sequence
of their incorporation into the peptide string. Amino acids differ in their size
depending on their side groups; their molecular weights can range from 75
daltons (a dalton is the mass of a hydrogen atom, a twelfth of a carbon atom) for
glycine, to about 200 daltons for tryptophan which contains a double aromatic
ring. Functional proteins also range in size: 55 kilodaltons (one kilodalton = one
thousand daltons) for tubulin monomers to 630 kilodaltons for thyroglobulin, to
several million kilodaltons for protein assemblies which comprise large viruses
and infectious agents of certain diseases like psittacosis and lymphogranuloma
venereum (Harper,1969). Thus proteins are comprised of several hundred to
millions of amino acids. The precise sequence of amino acids is determined by
DNA and they are assembled on ribosomes. A polypeptide “backbone” of 200
amino acids would have 22 200 different possible primary structures. The mass