This study is focus on the following matter: primary sequence, secondary sequence, tertiary sequence and quarternary sequence of the respective proteins. We also examined the nature, function and sources of each protein. Also, the role of LIM Domains in all the proteins is also will be discuss.
Introduction This study is focus on the following matter: primary sequence, secondary sequence, tertiary sequence and quarternary sequence of the respective proteins. We also examined the nature, function and sources of each protein. Also, the role of LIM Domains in all the proteins is also will be discuss. The proteins that used in this study have one thing in common: they are all protein structure of Lim Domain. The LIM domain is now recognized as a tandem zinc-finger structure that functions as a modular protein-binding interface. LIM domains are present in many proteins that have diverse cellular roles as regulators of gene expression, cytoarchitecture, cell adhesion, cell motility and signal transduction. An emerging theme is that LIM proteins might function as biosensors that mediate communication between the cytosolic and the nuclear compartments. The proteins used in this study are: Cysteine, Glycine, LASP-1 and Integrins-linked Kinase. At this part, let’s take a look at their nature, functions and sources: The first protein is Cysteine. It is named after Cystine, which comes from the Greek word “kustis” meaning bladder. It is unique among the twenty common amino acids because it contains a thiol group. Thiol groups can undergo oxidation of a pair of cysteine residues is oxidised produces cystine, a disulfide- containing derivative. Cysteine is an important source of sulfur in human metabolism, and although it is classified as a non-essential amino acid. It may be essential for infants, the elderly, and individuals with certain metabolic disease or who suffer from malabsorption syndromes. Cysteine is an important precursor in the production of glutathione in the body and other organisms. The systemic availability of oral glutathione (GSH) is negligible; the vast majority of it must be manufactured intracellularly. Glutathione is a tripeptide antioxidant made up of the three amino acids cysteine, glycine and glutamate. It can be found in eggs, meat, red peppers, garlic, onions, broccoli, brussel sprouts, oats, milk, whey protein, and wheat germ. However, it is not classified as an essential amino acid, and can usually be synthesized by the human body under normal physiological conditions if a sufficient quantity of methionine is available. The next one is Glycine. Glycine is the organic compound with the formula HO2CCH2NH2. It is one of the 20 amino acids commonly found in animal proteins. Its three letter code is gly, its one letter code is G, and its codons are GGU, GGC, GGA and GGG. Because of its structural simplicity, this compact amino acid tends to be evolutionarily conserved in, for example, cytochrome c, myoglobin, and hemoglobin. Most proteins contain only small quantities of glycine. A notable exception is collagen, which contains about one-third glycine. Glycine is an inhibitory neurotransmitter in the central nervous system, especially in the
Transcript
Introduction
This study is focus on the following matter: primary sequence, secondary sequence, tertiary sequence and quarternary sequence of the respective proteins. We also examined the nature, function and sources of each protein. Also, the role of LIM Domains in all the proteins is also will be discuss.
The proteins that used in this study have one thing in common: they are all protein structure of Lim Domain. The LIM domain is now recognized as a tandem zinc-finger structure that functions as a modular protein-binding interface. LIM domains are present in many proteins that have diverse cellular roles as regulators of gene expression, cytoarchitecture, cell adhesion, cell motility and signal transduction. An emerging theme is that LIM proteins might function as biosensors that mediate communication between the cytosolic and the nuclear compartments.
The proteins used in this study are: Cysteine, Glycine, LASP-1 and Integrins-linked Kinase. At this part, let’s take a look at their nature, functions and sources:
The first protein is Cysteine. It is named after Cystine, which comes from the Greek word “kustis” meaning bladder. It is unique among the twenty common amino acids because it contains a thiol group. Thiol groups can undergo oxidation of a pair of cysteine residues is oxidised produces cystine, a disulfide-containing derivative. Cysteine is an important source of sulfur in human metabolism, and although it is classified as a non-essential amino acid. It may be essential for infants, the elderly, and individuals with certain metabolic disease or who suffer from malabsorption syndromes. Cysteine is an important precursor in the production of glutathione in the body and other organisms. The systemic availability of oral glutathione (GSH) is negligible; the vast majority of it must be manufactured intracellularly. Glutathione is a tripeptide antioxidant made up of the three amino acids cysteine, glycine and glutamate. It can be found in eggs, meat, red peppers, garlic, onions, broccoli, brussel sprouts, oats, milk, whey protein, and wheat germ. However, it is not classified as an essential amino acid, and can usually be synthesized by the human body under normal physiological conditions if a sufficient quantity of methionine is available.
The next one is Glycine. Glycine is the organic compound with the formula HO2CCH2NH2. It is one of the 20 amino acids commonly found in animal proteins. Its three letter code is gly, its one letter code is G, and its codons are GGU, GGC, GGA and GGG. Because of its structural simplicity, this compact amino acid tends to be evolutionarily conserved in, for example, cytochrome c, myoglobin, and hemoglobin. Most proteins contain only small quantities of glycine. A notable exception is collagen, which contains about one-third glycine. Glycine is an inhibitory neurotransmitter in the central nervous system, especially in the spinal cord, brainstem, and retina. When glycine receptors are activated, chloride enters the neuron via ionotropic receptors, causing an Inhibitory postsynaptic potential (IPSP). Aminolevulinic acid, the key precursor to porphyrins is biosynthesized from glycine and succinoyl. Glycine is a sweet-tasting, non-essential amino acid that can be produced from serine and threonine, which means that it is manufactured in the liver; it does not have to be obtained directly through the diet.
The third protein is LASP-1. LASP1 is a cytoskeletal scaffold protein belonging to the LIM protein sub family. LASP1 consists of an N-terminal LIM domain, followed by two nebulin repeats, and a C-terminal SH3 domain. LASP1 plays an important role in the regulation of dynamic actin-based, cytoskeletal activities and cell motility. Agonist-dependent changes in LASP1 phosphorylation may also serve to regulate actin-associated ion transport activities, not only in the parietal cell but also in certain other F-actin-rich secretory epithelial cell types. Together, (LIM-) nebulette, Lasp-1, and zyxin may play an important role in the organization of focal adhesions. The protein is expressed in lymphocytes, neutrophils, macrophages, and endothelium and may regulate neutrophil motility, adhesion to fibrinogen matrix proteins, and transendothelial migration.
The last protein is Integrin-linked kinase (ILK) which is directly recruited to β1 and β3 integrin cytoplasmic domains. It was identified and cloned 6 yr ago based on its interaction with the β1 integrin cytoplasmic domain (Hannigan et al., 1996). ILK has been shown to play crucial roles in actin rearrangement, cell polarisation, spreading, migration, proliferation and survival (Legate et al., 2006). Despite its predominant localisation in FAs, ILK has also been shown to reside in cell–cell adhesion sites, in centrosomes and in the nucleus. ILK has been shown to serve as a scaffold
for promoting the formation of cell–cell contacts and the recruitment of tight junction proteins ( Vespa et al., 2003; Vespa et al., 2005). Genetic and biochemical evidence have established an essential role of ILK in connecting integrins to the actin cytoskeleton. Apart from integrins, ILK interacts with several adaptor and signaling proteins resulting in its activation and localization to focal adhesion plaques.The kinase activity of ILK is stimulated upon integrin engagement, as well as by growth factors and chemokines in a PI-3Kinase-dependent manner. ILK can mediate the phosphorylation of a variety of intracellular substrates, most notable of which are: protein kinase B (PKB/Akt), glycogen synthase kinase-3 (GSK-3) and myosin light chain.
1. Shape – the protein is shaped like a turtle from this view.
2. Domains: mesh = functional; lines = structural
3. Metal Cofactors and Interaction Zinc Ion
4. Additional Components ACE
2KBX Solution Structure of ILK-Pinch Complex 10-Dec-08
Author: J.QinMolecule (1): Integrin-linked Protein KinaseChain: AlphaMolecule (2): Lim and senescent cell antigen-like-containing domain protein 1Chain: BetaOrganism: Homo Sapiens / HumanMetal: Zinc ion
M 8 3.32 N 16 6.64D 15 6.22 A 24 9.96I 8 3.32 V 14 5.81F 12 4.98 L 20 8.30T 5 2.07 W 4 1.66Q 12 4.98 H 9 3.73C 11 4.56 S 6 2.50R 14 5.81 P 9 3.73E 18 7.47 Y 7 2.90G 18 7.47 K 11 4.56
4. Percentage of Polar / Nonpolar:
Sphere = polarLine = nonpolar
Frequency PercentagePolar 106 43.98
Nonpolar
135 56.02
Secondary
1. Alpha and Beta
Alpha (13)
Beta (4)
2. Residues for Alpha and Beta
Residues for Alpha (13)
Residues for Beta (4)
Red lines = AlphaBlue lines = BetaGreen cartoon = Random coil
3. Stabilizing Factors
Acid – Base
4. Random Coil
5. B-turn / Helix Bend
TERTIARY
1. Shape – frog-shaped protein
2. Domains: mesh = functional; lines = structural
3. Metal Cofactors and Interaction Spheres = Zinc Ions
Quarternary
1. Peptide Units – A (orange) and B (blue) peptide units
2. Interaction between units
They are connected through Hydrogen Bonding. (99) Histidine from peptide A and (38) Cystine from peptide B.
COMPARISON
The primary structure of the protein, 1ZFO, amino terminal lim dimain peptide of lasp-1, has 33
residues or amino acids. Its 0ph charge is +7, and when the pH increases and reach 13 pH, the charge will be -6.
1ZFO is the only protein that 0 charge in 8.3 pH level. Its P.I is 9.2. The most frequent amino acid in the sequence
are lysine (K) and cysteine (C) that is both 13.33%. 1ZFO is non-polar (73.33%), an alpha chain therefore, it is
hydrophobic. 1A7I, amino terminal lim domain from quail cysteine and glycine, has 61 residues or amino acids.
Its 0pH level charge is +13, and as the pH increases and reach the level 13pH the charge will be -26. This protein
has no 0 charge pH level or the zwitter ion. The most frequent amino acid is cysteine (C) that is 15% of the
sequence. 1A7I is non polar (55%), therefore it is also an alpha chain and is hydrophobic. 1CTL, carboxyl-
terminal lim domain from the cysteine rich protein CRP, has 85 residues or amino acids. Its 0pH level charge is
+15, and as the pH increases and reach the level 13, the charge will be -25. This protein also has no zwitter ion.
The most frequent amino acid is glycine (G) that is17.65% of the sequence. 1CTL is also non polar, an alpha chain
and is hydrophobic. 2KBX, solution structure of ILK-Pinch complex, has 241 residues or amino acids. Its 0pH
level charge is +35, as the pH increases and reach the 13pH level the charge will be -63. This protein has no
zwitter ion. The most frequent amino acid is leucine (L) that id 8.30 % of the sequence. 2KBX has an alpha chain
and beta chain, non polar amino acid is 135 or 56.02% and the polar amino acids is 43.98% of the sequence.
For the secondary structure, the protein with the highest number of alpha is the solution structure of ILK-Pinch
Complex that can be found in humans, having thirteen (13) alphas. While the protein amino-terminal lim domain
peptide of LASP-1, NMR that can be found in the intestines of a pig, has two (2) alphas and the proteins carboxy-
terminal Lim Domain from the Cysteine rich protein CRP that can be found in chickens and amino-terminal Lim Domain
from Quail Cysteine and Glycine has both one (1) alpha. But the protein with the highest number of beta is carboxy-
terminal Lim Domain from the Cysteine rich protein CRP, having eight (8) betas, while all 3 remaining proteins have four
(4) betas. The protein amino-terminal Lim Domain from Quail Cysteine and Glycine, is basic. It has a residue of the amino
acids glutamic acid, histidine, and lysine. The protein carboxy-terminal Lim Domain from the Cysteine rich protein CRP is
also a basic. It has a residue of the amino acids glutamic acid, histidine, lysine, arginine and aspartic acid. The protein
amino-terminal Lim domain peptie of LASP-1 NMR is also basic. It also has a residue of the amino acids glutamic acid,
histidine, lysine. Lastly, the protein that can be found in humans which is the solution structure of ILK-Pinch Complex is
still basic. It has residues of arginine, aspartic acid, glutamic acid and histidine. The amino-terminal lim domain from
quail cysteine and glycine has six (6) random coils while carboxy-terminal lim domain from the cysteine rich protein CRP
has nine (9) random coils, the amino-terminal lim domain peptide of LASP-1 has only three (3) random coils, and the
solution structure of ILK-Pinch Complex has fourteen (14) random coils. The amino-terminal lim domain from quail
cysteine and glycine turned five (5) times, while carboxy-terminal lim domain from the cysteine rich protein CRP turned
thirteen (13) times. The amino-terminal lim domain peptide of LASP-1 only turned once (1) while the solution structure
of ILK-Pinch Complex turned fifteen (15) times.
REFERENCES:
Cysteine Bulaj G, Kortemme T, Goldenberg D (1998). "Ionization-reactivity relationships for cysteine thiols in
polypeptides.".Biochemistry 37 (25): 8965-72. PMID 9636038. Baker D, Czarnecki-Maulden G (1987). "Pharmacologic role of cysteine in ameliorating or exacerbating mineral
toxicities.". J Nutr 117 (6): 1003-10. PMID 3298579. Retrieved October 5, 2014 from http://www.ammunotec.com/glutathione.html
Glycine Kuan YJ, Charnley SB, Huang HC, et al. (2003) Interstellar glycine. ASTROPHYS J 593 (2): 848-867 Snyder LE, Lovas FJ, Hollis JM, et al. (2005) A rigorous attempt to verify interstellar glycine. ASTROPHYS J 619 (2):
914-930 Safety (MSDS) data for glycine. The Physical and Theoretical Chemistry Laboratory Oxford University (2005).
Retrieved on 2006-11-01. Dawson, R.M.C., Elliott, D.C., Elliott, W.H., and Jones, K.M., Data for Biochemical Research (3rd edition), pp. 1-31
(1986) Campbell, W. R. (2012). Glycine : The amino acid that is necessary for central nervous system function and a
healthy prostate. Retrieved October 5, 2014 from http://blissreturned.wordpress.com/2012/04/09/glycine-the-amino-acid-that-is-necessary-for-central-nervous-system-function-and-a-healthy-prostate/
LSP Retrieved October 5, 2014 from http://www.ncbi.nlm.nih.gov/gene/4046 Tomasetto, C. et al. (1995) FEBS Lett 373, 245-9. Schreiber, V. et al. (1998) Mol Med 4, 675-87. Chew, C.S. et al. (2002) J Cell Sci 115, 4787-99. Lin, Y.H. et al. (2004) J Cell Biol 165, 421-32. Frietsch, J.J. et al. (2010) Br J Cancer 102, 1645-53. Traenka, C. et al. (2010) Cancer Res 70, 8003-14.
ILK Hannigan, G. E., Leung-Hagesteijn, C., Fitz-Gibbon, L., Coppolino, M. G.,Radeva, G., Filmus, J., Bell, J.
C. and Dedhar, S. (1996). Regulation of cell adhesion and anchorage-dependent growth by a new beta 1-integrin-linked protein kinase. Nature 379, 91-96.
Legate, K. R., Montañez, E., Kudlacek, O. and Fässler, R.(2006). ILK, PINCH and parvin: the tIPP of integrin signalling. Nat. Rev. Mol. Cell Biol. 7,20-31.
Vespa, A., Darmon, A. J., Turner, C. E., D'Souza, S. J. and Dagnino, L.(2003). Ca2+-dependent localization of integrin-linked kinase to cell junctions in differentiating keratinocytes. J. Biol. Chem. 278, 11528-11535.
Dedhar, P.S. (2003). The role of integrin-linked kinase(ILK) in cancer progression. Thesis. Retrieved October 5, 2014 from http://www.ncbi.nlm.nih.gov/pubmed/12884912
LIM Domain
Kadrmas, J.L and Beckerle, M.C. (2004). The Lim domain: from the cytoskeleton to the nucleus. Nat. Re. Mo. Cell Biol. 5, 920-931
