Proline isomerization in epigenetics
In epigenetics, proline isomerization is the effect that cis-trans isomerization of the amino acid proline has on the regulation of gene expression. Similar to aspartic acid, the amino acid proline has the rare property of being able to occupy both cis and trans isomers of its prolyl peptide bonds with ease. Peptidyl-prolyl isomerase, or PPIase, is an enzyme very commonly associated with proline isomerization due to their ability to catalyze the isomerization of prolines. PPIases are present in three types: cyclophilins, FK506-binding proteins, and the parvulins. PPIase enzymes catalyze the transition of proline between cis and trans isomers and are essential to the numerous biological functions controlled and affected by prolyl isomerization Without PPIases, prolyl peptide bonds will slowly switch between cis and trans isomers, a process that can lock proteins in a nonnative structure that can affect render the protein temporarily ineffective. Although this switch can occur on its own, PPIases are responsible for most isomerization of prolyl peptide bonds. The specific amino acid that precedes the prolyl peptide bond also can have an effect on which conformation the bond assumes. For instance, when an aromatic amino acid is bonded to a proline the bond is more favorable to the cis conformation. Cyclophilin A uses an "electrostatic handle" to pull proline into cis and trans formations. Most of these biological functions are affected by the isomerization of proline when one isomer interacts differently than the other, commonly causing an activation/deactivation relationship. As an amino acid, proline is present in many proteins. This aids in the multitude of effects that isomerization of proline can have in different biological mechanisms and functions.
Cell signaling
Cell signaling involves many different processes and proteins. One of the most studied cell signaling phenomena involving proline is the interactions with p53 and prolyl isomerases, specifically Pin1. The protein p53, along with p63 and p73, are responsible for ensuring that alterations to the genome are corrected and for preventing the formation and growth of tumors. proline residues are found throughout the p53 proteins and without the phosphorylation and isomerization of specific Serine/Threonine-Proline motifs within p53, they cannot exhibit control over their target genes. The main signalling processes that are affected by p53 are apoptosis and cell cycle arrest, both of which are controlled by specific isomerization of the prolines in p53.History and discovery
Although isomerization of proteins has been known about since 1968 when it was discovered by C. Tanford, proline isomerization and its use as a noncovalent histone tail modification was not discovered until 2006 by Nelson and his colleagues.As a histone tail modification
One of the most well known epigenetic mechanisms that proline isomerization plays a role in is the modification of histone tails, specifically those of histone H3. Fpr4 is a PPIase, in the FK507BP group, that exhibits catalytic activity at the proline positions 16, 30, and 38 on the N-terminal region of histone H3 in Saccharomyces cerevisiae. Fpr4's binding affinity is strongest at the P38 site, followed by P30 and then P16. However the catalytic efficiency, or the increase in isomerization rates, is highest at P16 and P30 equally, followed by P38 which exhibits a very small change in isomerization rates with the binding of Fpr4. Histone H3 has an important lysine residue at the 36 position on the N-terminal tail which can be methylated by Set2, a methyltransferase. Methylation of K36 is key to normal transcription elongation. Due to P38's proximity to K36, cross-talk between P38 isomerization and K36 methylation can occur. This means that isomer changes at the P38 position can affect methylation at the K36 position. In the cis position, P38 shifts the histone tail closer to the DNA, crowding the area around the tail. This can cause a decrease the ability of proteins to bind to the DNA and to the histone tail, including preventing Set2 from methylating K36. Also, this tail movement can increase the number interactions between the histone tail and the DNA, increasing likelihood of nucleosome formation and potentially leading to the creation of higher-order chromatin structure. In trans, P38 leads to the opposite effects: allowing for Set2 to methylate K36. Set2 is only affected by isomerization of P38 when creating a trimethylated K36, however, and not K36me2. Fpr4 also binds to P32 in H4, though its effects are minimal.In mammalian cells, the isomerization of H3P30 interacts with the phosphorylation of H3S28 and the methylation of H3K27. hFKBP25 is a PPIase that is a homolog for Fpr4 in mammalian cells and is found to commonly be associated with the presence of HDACs. Cyp33 is a cyclophilin that has the ability to isomerize H3 proline residues at P16 and P30 positions. Histones H2A and H2B also have multiple proline residues near amino acids that when modified affect the activity surrounding the histone.