Ron Raines, Ph.D., professor of biochemistry of the University of Wisconsin in Madison, talked about the effects of stereoelectronics on peptide and protein conformation at the Gordon Research Conference on the “Chemistry and Biology of Peptides.”
“Collagen comprises one-third of total protein and is the most prevalent component of the extracellular matrix. Twenty-eight different types of collagen composed of at least 46 distinct polypeptide chains have been identified in vertebrates and many other proteins contain collagenous domains.”
Indeed, collagen is the major component of skin and other fibrous tissues, and an understanding of the modifications that take place in the course of the aging process are vital for a thorough understanding of how these events affect the longevity of the individual.
This ubiquitous molecule is defined by a structural motif in which three parallel polypeptide strands coil about each other to form a right-handed triple helix. Every third residue of the amino acid sequence of collagen is glycine, so the repeating order is XaaYaaGly. The most common residents of the X and Y positions are proline and hydroxyproline. This sequence of amino acids gives rise to the 3-D conformation of the molecule and endows it with its characteristics of insolubility and durability.
Whole collagen molecules are difficult to study at atomic resolution. As a result, Dr. Raines and his team have focused on peptides to obtain a detailed picture of collagen’s 3-D structure. Their investigations have elucidated the role of stereoelectronic effects on peptide and protein conformation, that is, the chemical consequences of orbital overlap, a phenomenon that can play a significant role in the structure and function of organic molecules.
Dr. Raines’ studies have also revealed simple mechanisms for the synthesis of long collagen triple helices and fibrils, which in years to come could play an essential role in biomedicine and nanotechnology. Indeed, early animal studies have revealed that synthetic, stronger collagen fibrils can expedite wound healing, anchoring growth factors more effectively and speeding the growth of new skin.
Other investigations by Dr. Raines’ lab have revealed that collagen-related molecules can be coated with gold and other conductive metal to form nanowires. In the future these might form constituents of nanodevices that could be used to repair damaged tissues and monitor internal physiological conditions.
Andrei Yudin, Ph.D., professor at the University of Toronto, discussed the properties of natural and synthetic cyclic peptides, molecules that have found utility in a variety of pharmaceutical and industrial applications. Because these structures can act as nanomaterials, imaging agents, and drug candidates, there is great interest in their properties.
Dr. Yudin explained that peptides have a zwitterionic nature, that is, they are both positively and negatively charged, with the amino end of the molecule positive and the C-terminal being negative. So even though cyclization of peptides is not thermodynamically favored, enthalpic contributions from electrostatic and polar interaction can drive the formation of ring structures. In the case of small peptides (<7 amino acids), amphoteric molecules that can behave as both an electrophile and a nucleophile can be used to promote peptide cyclization.
It is well known that conventional activation reagents remove the zwitterionic character of the peptide. To achieve the preferred reaction in a workable timeframe, Dr. Yudin’s group employed the “Ugi Reaction,” which favors the thermodynamic equilibrium of amide bond formation. Using an amphoteric amino aldehyde, the product is a cyclic peptide molecule that can facilitate the synthesis of peptides with a range of amino acids.
“Amphoteric amino aldehydes have led to the development of a novel peptide macrocyclization process. The resulting molecules possess useful structural features that allow specific modifications such that fluorescent tags, solubilizing groups, and conformation tuning. Given the prevalence of cyclic peptides in chemistry and biology, this operationally simple method should find utility in many areas.
“Furthermore, the method should be adaptable to other linear molecule substrates, leading to a wide range of novel macrocyclic architectures, for instance cyclic oligonucleotides.”