Protein pattern

Protein-pattern databases cover both motifs or functional domains and secondary structure. We have included the entire InterPro family of databases, as well as BLOCKS, CDD, and a description of patterns found in Swiss-Prot sequences. DSSP, ISSD, PSSD, and CATH are covered in the secondary-structure section. 

UniProt is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR. UniProt is comprised of three components, each optimized for different uses. The UniProt Knowledgebase (UniProt) is the central access point for extensive curated protein information, including function, classification, and cross-reference. The UniProt Non-redundant Reference (UniRef) databases combine closely related sequences into a single record to speed searches. The UniProt Archive (UniParc) is a comprehensive repository, reflecting the history of all protein sequences. 

Each InterPro entry includes a match table listing UniProt protein sequences matching the entry s signature(s). 

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Vartanian, N., Damerval, G. de Vienne, D. (1987). Drought-induced changes in protein patterns of Brassica napus var. oleifera roots. Plant Physiology, 84, 989-92. 

Parthasaralhy, R. and Groves, J. T. (2004) Protein patterns at lipid bilayer junctions. Proc. Natl. Acad. Sci. USA, 101, 12798-12803. 

Fuchs E., Rosenbusch J. and Anzenberger G. (1991). Urinary protein pattern reflects social rank in male Common Marmosets. Folia Primatol (Basel) 57, 177-180. 

Apart from its natural occurrence, Co may find its way into other proteins either adventitiously or deliberately. A study was undertaken where the blood, serum, and plasma of workers occupationally exposed to Co were analyzed for the element.1189 When separated by gel electrophoresis under denaturing conditions, the Co fractions in all blood, serum, and plasma samples showed a similar protein pattern. A variety of proteins of differing size were found to bind Co in fractions collected at pFl 5, whereas only hemoglobin was found in the pH 7 fractions. The conclusions were that in vivo Co is bound to plasma proteins, perhaps albumin and hemoglobin. 

Arce A et al. Changes in the liver protein pattern of female Wistar rats treated with the hypoglycaemic agent SDX PGU 693. Life Sci 1998 63 2243-2250. 

Cruz-Ortega, R., Ayala-Cordero, G. and Anaya, A.L. (2002). Allelochemical stress produced by Callicarpa acuminata effects on catalase activity and protein pattern synthesis of crop plants. Physiologia Plantarum 116 20-27... 

Fig. 11.3 Data from an MD Class BioCD. (a) Time trace of gold spokes on an antinode dielectric disk with alternating immobilized antibody. A half harmonic sine wave is shown for comparision. (b) Power spectrum of the signal, showing the carrier frequency and the half harmonic protein pattern...

A drawback of the MD-class BioCD is the microfabrication required to pattern gold spokes on the disc to set the quadrature condition. To remove the microfabrication, an alternative means to establish a quadrature condition uses adaptive optical mixers in the far field to establish and lock phase quadrature. In this case, the disc can be a high-reflectance antinode surface with protein patterned directly on the disc surface without any need for surface structuring. As the disc spins, the immobilized protein causes phase modulation that is detected in the quadrature condition set up by the adaptive mixer. 

Atsuta, K. Suzuki, H. Takeuchi, S., A parylene lift off process with microfluidic channels for selective protein patterning, J. Micromech. Microeng. 2007, 17, 496 500... 

M. Ramstrom, I. Ivonin, A. Johansson, H. Askmark, K. E. Markides, R. Zubarev, P. Hakansson, S.-M. Aquilonius, and J. Bergquist. Cerebrospinal Fluid Protein Patterns in Neurodegenerative Disease Revealed by Liquid Chromatography Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. Proteomics, 4(2004) 4010-4018. 

Electrophoresis of the urine in these cases with more massive proteinuria shows a protein pattern resembling plasma (K13). 

Fig. 1. Schematic presentation of the protein pattern of the common Hp types in pure form after starch-gel electrophoresis. The protein pattern of a normal serum belonging to Hp type 1-1 is given at the bottom. The cathodic part is excluded.

In order to quantitatively analyze the protein patterns, the gels were scanned, and the relative optical density of the bands was plotted against the distance from the start of the gel. 

More recent electrophoretic studies 13,14,15 have all yielded evidence which clearly demonstrates that the plasma protein patterns as determined in this manner are distinctive for each individual. 

Witzmann FA (1994) Two-dimensional protein pattern recognition in chemical toxicity. Government Reports Announcements Index (GRA I) Issue 19 NTIS/AD-A280 359/1, p 47... 

For proper identification of the proteins of interest in a blot, immunodetected proteins must be compared to the total protein pattern of the gel. This requires the indiscriminate staining of all the proteins in the blot. Colloidal gold stain is... 

VanAdrichem J.H.M., Bomson K.O., Conzelmann H., Gass M.A.S., Eppenberger H., Kresbach G.M., Ehrat M., and Leist C.H. (1998), Investigation of protein patterns in mammalian cells and culture supernatants by matrix assisted laser desorption/ionization mass spectrometry, Anal. Chem. 70, 923-930. 

Only a very small reduction in the number of acid-insoluble SH-groups in platelets was seen in the presence of feverfew extract [52]. A change in the high molecular weight protein pattern was only seen after the platelets had been activated. Such changes are indicative of polymerization of the proteins and the formation of S-S bridges and this can lead to disturbances in membrane-cytoskeletal interactions. Uptake of [ " C]arachidonic acid into phospholipids was inhibited by feverfew [53], which may be a result of altered cytoskeletal-membrane interaction. 

In healthy individuals, the concentration of plasma proteins is constant. Diseases in organs that are involved in protein synthesis and breakdown can shift the protein pattern. For example, via cytokines (see p. 392), severe injuries trigger increased synthesis of acute-phase proteins, which include C-reac-tive protein, haptoglobin, fibrinogen, complement factor C-3, and others. The concentrations of individual proteins are altered in some diseases (known as dysproteinemias). 

A7. Anderson, C. G., and Altman, A., The electrophoretic serum protein patterns in malignant malnutrition. Lancet i, 203-204 (1951). 

Stonard MD, Gore CW, Oliver JA, et al. 1987. Urinary enzymes and protein patterns as indicators of injury to different regions of the kidney. Fund AppI Toxicol 9 339-351. 

Starting with a single pre-mRNA several alternative mRNAs via the rejoining of various exons can be formed, each coding for proteins with different activities and functions. The creation of different proteins due to alternative splicing is a commonly used tool for cell- and tissue-specific expression of proteins. By the formation of variable spliced proteins, a tissue-specific constitutive protein pattern can be created. An example for this is shown in Fig. 1.48. Alternative splicing can also be used to rapidly and flexibly adjust the expression of specific proteins in response to a transduced external signal. 

Maximum reproducibility of 2-DE protein patterns in large-scale proteome analysis can be achieved by simultaneous electrophoresis of SDS-PAGE. Amersham Pharmacia Biotech (Piscataway, NJ) firm developed a multiple vertical second-dimension... 

Proteomics has the potential to revolutionize diagnosis and disease management. Profiling serum protein patterns by means of surface-enhanced laser desorption/ion-isation time of flight (SELDI-TOFF) mass spectrometry is a novel approach to... 

Bortree, A. L., Carroll, E. J. and Schalm, 0. W. 1962. Whey protein patterns of milk from cows with experimentally produced mastitis. J. Dairy Sci. 45, 1465-1471. 

Leece, J. G. and Legates, J. E. 1959. Changes in the paper electrophoretic whey-protein pattern of cows with acute mastitis. J. Dairy Sci. 42, 698-704. 

Locate the glycoprotein band of interest on the membrane by companng the total protein pattern with glycoprotein pattern obtained as described in the previous subsection. 

Proteins, blotted from polyacrylamide gels onto nitrocellulose sheets (Western blots) can be stained nonspecifically with a variety of dyes, or they can be identified individually by probing with appropriate antibodies. These procedures may be performed on duplicate blots, staining the total protein pattern on one blot and using the second blot for the immune reaction (1,2) This chapter describes how to combine both methods on one blot, i.e., staining the blot first for total protein, followed by an indirect immune reaction (3). 

Locating immunoreactive proteins or protein A-containmg fusion proteins on the blot in relation to the total protein pattern of a given sample ... 

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