Sandbox Reserved 654
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<Structure load='1JM4' size='500' frame='true' align='right' caption='This is a model of the pheylalanine hydroxylase dimer as found in humans. The green ball in within each subunit represents the iron ion in the catalytic domains.' scene='Insert optional scene name here' /> | <Structure load='1JM4' size='500' frame='true' align='right' caption='This is a model of the pheylalanine hydroxylase dimer as found in humans. The green ball in within each subunit represents the iron ion in the catalytic domains.' scene='Insert optional scene name here' /> | ||
- | + | The bromodomain is an evolutionary conserved motif found in chromatin remodeling complexes. It has been found in over 100 proteins from multiple organisms ranging from unicellular microscopic eukaryotes (e.g., yeast) to humans. The motif is best known for the groundbreaking recent discoveries made to identify it as the only acetyl-lysine binding domain, Dhalluin, C. et al (1999) Nature 399, 491, and to reveal its highly specific ligand selectivity properties. Zeng, L. (2002) FEBS 513:1, 124. Due to these novel characteristics, bromodomains are typically found in proteins responsible for modifications in chromatin structure and the regulation of gene expression, such as histone acetyltransferases (HATs), and the ATPase subunits of chromatin remodeling complexes. There are several families of proteins with bromodomains. One such family is the human transcriptional coactivator p300/CBP-associated factor (PCAF) bromodomain, <ref> sample ref </ref> | |
== '''Structure and Function''' == | == '''Structure and Function''' == |
Revision as of 01:00, 18 November 2012
This Sandbox is Reserved from 30/08/2012, through 01/02/2013 for use in the course "Proteins and Molecular Mechanisms" taught by Robert B. Rose at the North Carolina State University, Raleigh, NC USA. This reservation includes Sandbox Reserved 636 through Sandbox Reserved 685. | |||||||||||||
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Introduction
The bromodomain is an evolutionary conserved motif found in chromatin remodeling complexes. It has been found in over 100 proteins from multiple organisms ranging from unicellular microscopic eukaryotes (e.g., yeast) to humans. The motif is best known for the groundbreaking recent discoveries made to identify it as the only acetyl-lysine binding domain, Dhalluin, C. et al (1999) Nature 399, 491, and to reveal its highly specific ligand selectivity properties. Zeng, L. (2002) FEBS 513:1, 124. Due to these novel characteristics, bromodomains are typically found in proteins responsible for modifications in chromatin structure and the regulation of gene expression, such as histone acetyltransferases (HATs), and the ATPase subunits of chromatin remodeling complexes. There are several families of proteins with bromodomains. One such family is the human transcriptional coactivator p300/CBP-associated factor (PCAF) bromodomain, [1] Structure and FunctionThe bromodomain was originally identified as a sequence of roughly 60 amino acid residues that forms 2 alpha helices. Haynes, S.R. et al (1992) Nucleic Acids Res. 20, 2603. However, it is now known that the bromodomain consist of a highly conserved sequence of approximately 110 amino acids. Owen, D. J. et al. (2000) EMBO J. 19(22), 6141. The structure of the PCAF bromodomain consists of a four-helix bundle (alphaZ, aA,aB, and aC) with a left-handed twist, and a long intervening loop between helices Z and A (ZA loop). Dhalluin. The ZA loop of the bromodomain has a defined conformation and is packed against the loop between helices aB and aC (BC loop) to form a hydrophobic pocket. This pocket created by the ZA and BC loops is lined by specific residues (Val 752, Ala 757, Tyr 760, Val 763, Tyr 802 and Tyr 809) that support protein-protein interactions. The ZA loop varies in length between different bromodomains, but almost always contains residues corresponding to Phe 748, Pro 751, Pro 758, Tyr 760 and Pro 767. Dhalluin. The hydrophobic pocket formed by the loops is the primary binding site for acetyl-lysine proteins. This interaction has been shown via localization and chemical shift experiments that revealed the specific manner with which the bromodomain hydrophobic cavity binds to acetylated lysine residues. Once the acetyl-lysine residue makes the initial binding inside the hydrophobic pocket, the ZA and BC loop residues at the entrance of the pocket interact with the amino acids adjacent (+/- 1 or 2) to the already bound acetyl-lysine. Those interactions reinforce binding of the target sequence. Mujtaba, S. et al (2007) Oncogene 26, 5521. Small structural changes in the conformation of the ZA and BC loops result in exposing other residues that are originally buried within the protein to aid in peptide recognition. Mujtaba, S. et al (2002) Mol. Cell 9, 575. MechanismThe mechanism of protein-protein interaction for the bromodomain of PCAF with histone proteins begins with the acetylation of lysine residues on the histone tail. The acetylation causes a conformational change in the histones, which allows for transcriptional machinery to access DNA. The bromodomains of PCAF within a pretranscriptional initiation complex (PIC) bind to the acetyl-lysine of the histone to stabilize the complex so that transcription may begin. The bromodomains of PCAF have three major points of contact that allow for site-specific histone recognition. First, the acetylated lysine of the target protein enters a hydrophobic pocket embedded between the ZA and BC loops at the bottom of the protein. The Asn803 residue in the bromodomain forms a hydrogen bond with the amide nitrogen of the acetyl-lysine. Next, residues in the ZA and/or BC loops interact with residues adjacent to the acetyl-lysine, which reinforces the acetyl-lysine binding in the bromodomain. Finally, additional residues in the ZA and BC loops that face opposite to the bromodomain form hydrophobic and/ or electrostatic interaction with the target protein 3 residues away from the acetyl-lysine. This residue clamps on the BC loop together with the acetyl-lysine side chain that is bound inside the hydrophobic pocket of the bromodomain.[5]
Implications or Possible ApplicationsThe first diagnosed cases of Phenylketonuria (PKU), otherwise known as Folling's Disease, were identified in 1934 by Norwegian doctor and biochemist Asbjorn Folling. Dr. Folling found that the urine of two of his young mentally handicapped patients contained a high level of phenylalanine. Follwing this discovery, it was found that the absence or malfunction of the phenylalanine hydroxylase enzyme is due to the mutation of the PAH gene and inherited autosomal recessively. This may result in a genetic disorder known as Phenylketonuria (PKU). This information was not utilized until the early 1950s when it was found that under a low phenylalanine diet, some of the symptoms found in children suffering from PKU could be reversed. Due to a diet rich in phenylalanine, this enzyme is vital in the regulation in phenylalanine plasma concentration by converting about 75% of the amino acid to tyrosine. Excessive amounts of phenylalanine has been shown to cause mental retardation in humans. Presently, it is regulation to screen newborns children for phenylketonuria with a simple blood or urine test. [2] Due to his discovery and development of the PKU test, Dr. Folling is remembered as one of the most important medical scientists that has not received a Nobel Prize for Physiology or Medicine. [3] Symptoms
Phenylalanine plays a variety of roles in the body among which is the production of melanin, the pigment responsible for hair and skin color. Infants with an overabundance of this residue may therefore have a lighter skin, hair and eye color than those who do not. [4] Other symptoms may include: - Delayed mental and social skills - Head size significantly below normal - Hyperactivity - Jerking movements of the arms or legs - Mental retardation - Seizures - Skin rashes - Tremors - Unusual positioning of hands TreatmentTreatment for such a PKU is a low phenylalanine diet and early detection. Those who start the diet early and adhere to it will have better mental and physical health. Infants diagnosed with the disease can fed a specially made formula called Lofenalac while others should follow a diet plan as illustrated in the image to the left. The main rule to follow is to avoid protein sources rich in phenylalanine and sugars containing aspartame. Taking extra supplements like fish oil can replace the fatty acids missing from the phenylalanine free diet and may also improve neurological development. PKU can also be caused by a deficiency in or inability to regenerate tetrahydrobipternin, the cofactor essential to the function of PheOH. Although this is not usually the cause of PKU, patients can be treated by taking tetrahydrobiopterin supplements. If the diet is not strictly followed, mental retardation may result after the first year of life. [5]
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