Life, in its entirety, is based on some fairly simple classes of chemical compounds: water, salts and some metals, lipids, amino and nucleic acids. For example, the most simple speck of life is a virus. Generally, viruses are composed of an outer protein coat surrounding an inner DNA or RNA strand. Proteins and DNA are the biological analogs of polymers. The basic subunits of proteins are amino acids and those of DNA or RNA are nucleic acids. There are twenty amino acids and five nucleic acids. These subunits can bond to form biopolymeric chains numbering in the millions. Although DNA or RNA are necessary for cellular replication and the propagation of a species genome and phenotypic characteristics, these comprise less than one percent of an entire organism. Proteins, however, comprise the structural, protective, catalytic, and metabolic core of an organism. It is proteins, and their diverse and complex role in life, that inspires the Peptide Dynamics Project, herein known as the PDP.
Any motion of an object with mass within a potential exhibits energy. Energy is the most fundamental observable property of the universe. Energy can do work, produce a force, and change the state of matter. For example, the frictional force of walking will create a small amount of heat in the foot print and the bottom of the shoe, which can be measured with a sensitive thermometer, thermocouple, or infrared detector.
A system will react when different forms or levels of energy are imposed upon it. The observation and measurement of the system’s response to the imposed energy will reveal new quantum mechanical properties and chemical characteristics of the system. Additionally, the flow of the imposed energy will reveal how the excess energy moves through the system, for the system will naturally dissipate the energy to return to its most relaxed state. An example of this is when light hits the chlorophyll pigment of a leaf. The absorbed energy is immediately captured and converted into chemical (ATP) energy, which is directly usable by the cell of the plant.
All normal matter is a vast empty black space, a void, with positive nuclei more than a thousand times smaller than the atom itself, and the negative electron orbitals creating the outer envelope of the atom. Matter is nothing more than a sea of moving invisible charge and all stuff, all stuff, is made of matter. Positive nuclei are swimming in a quantized sea of negative electron orbitals. Therefore, it is natural to study this sea of charge potential with an electric field, the most simple probe for studying charge known to science. Impedance or dielectric spectroscopy is the technique of imposing an electric field and studying its effect on a sample or material.
Classical spectroscopic techniques have imposed high energy levels on peptides and proteins in the infrared, visible, and ultra-violet electromagnetic regions to locally excite specifically bound chromophores, i.e. IR, UV-Vis, and laser spectroscopies. It is the intention of the PDP to impose ultra-low, sub-radio, electromagnetic energy to peptide segments and entire proteins and observe the dissipation of the absorbed energy throughout the system. This sub-radio technique is known as impedance or dielectric spectroscopy. Dielectric spectroscopy is an advancement in measuring the complex capacitance of a sample.
The development of infrared spectroscopy included a period of experimentation to empirically categorize specific energy signatures with organic functional groups and interactions, such as the presence of a methyl group or the steric hindrance of neighboring freely rotating methyl groups. Ultimately, the hope of the PDP is to perform a similar cataloging of peptide groups and protein structural motifs to specific energy signatures using impedance spectroscopy. The PDP Catalog will then be used to study unknown responses in unknown proteins or other biomolecules, or to further study enzymatic, receptor, or binding-site interactions.
The PDP website and proposal are written for a broad audience. The sections are divided to meet the needs of various interests and levels of scientific expertise. Each section is designed to provide an in-depth analysis of impedance spectroscopy, proteins, and the expected response from these systems of study and this instrumental technique.