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Topic: Protein methods

	Protein structure prediction - Wikipedia, the free encyclopedia
		The output of experimentally determined protein structures, typically by time-consuming and relatively expensive X-ray crystallography or NMR spectroscopy, is lagging far behind the output of protein sequences.
		Given the amino acid sequence of a unknown structure and the solved structure of a homologous protein, each amino acid in the solved structure is mutated, computationally, into the corresponding amino acid from the unknown structure.
		Protein threading scans the amino acid sequence of an unknown structure against a database of solved structures.
	en.wikipedia.org /wiki/Protein_structure_prediction (737 words)

	[No title] (Site not responding. Last check: 2007-11-05)
		This method involves biotinylation of the target cell, attachment of an avidin group to the protein to be transferred, and combining the biotinylated target cell and the avidin-tagged protein.
		The fusion protein is comprised of a first domain having affinity for the lipidated protein and a second domain of a peptide, protein, or derivative or fragment thereof, having trans signaling and/or adhesion function.
		The method of Claim 1, wherein said first protein is selected from the group consisting of lipidated protein A and lipidated protein G. The method of Claim 7, wherein said first protein is palmitated protein A. The method of Claim 1, wherein said first domain is attached at the amino terminus of said second protein.
	www.wipo.int /cgi-pct/guest/getbykey5?KEY=01/49825.010712&ELEMENT_SET=DECL (7084 words)

	PROTONET : Methods
		The foundation for the classification of proteins is a calculation of 'all-against-all' similarity for the set of proteins.
		The TrEMBL protein is initally attached ("hung") to the leaf of this Swiss-Prot protein in the ProtoNet tree.
		Then, the TrEMBL protein iteratively ascends in the path from this leaf to the root, as long as its addition to the parent cluster (of its cluster in the previous iteration) improves the merging score of the parent cluster.
	www.protonet.cs.huji.ac.il /methods.php?global=no\|3\|24\|lifetime\|1\|2\|2 (679 words)

	Methods in protein separation (Site not responding. Last check: 2007-11-05)
		Proteins of opposite charge to the matrix bind to the beads, while the rest flow through freely.
		The bound proteins are released from the matrix by an increase in salt concentration.
		Proteins are flowed over a column of beads coated with an antibody or other molecule that binds specifically to the protein you want to purify.
	yakko.bme.virginia.edu /biom204/notes/methods_notes.htm (659 words)

	Protein Arrays (Site not responding. Last check: 2007-11-05)
		Protein arrays are rapidly becoming established as a powerful means to detect proteins, monitor their expression levels, and investigate protein interactions and functions.
		Protein arrays have been designed as a miniaturisation of familiar immunoassay methods such as ELISA and dot blotting, often utilising fluorescent readout, and facilitated by robotics and high throughput detection systems to enable multiple assays to be carried out in parallel.
		Orientation of the surface-bound protein is recognised as an important factor in presenting it to ligand or substrate in an active state; for capture arrays the most efficient binding results are obtained with orientated capture reagents, which generally requires site-specific labelling of the protein.
	www.functionalgenomics.org.uk /sections/resources/protein_arrays.htm (4427 words)

	2D Protocols
		Proteins are loaded at the cathode on the first dimension gel and electrophoresed at 500 volts for 15 minutes and then 1500 volts for 2 hours.
		Proteins are stained overnight with 0.2% (w/v) Coomassie brilliant blue R250 in 50% (v/v) methanol, 5% (v/v) acetic acid; the gels are then destained in the same solution without the stain.
		Alternatively, the proteins are stained using the colloidal staining method described by Anderson et al.
	www.abdn.ac.uk /~mmb023/protocol.htm (1369 words)

	Protein sequencer - Wikipedia, the free encyclopedia
		A protein sequencer is a machine that is used to determine the sequence of amino acids in a protein.
		This is done repetitively for the whole polypeptide, until the whole sequence is established.
		This method has generally been replaced by nucleic acid technology, and it is often easier to identify the sequence of a protein by looking at the DNA that codes for it.
	en.wikipedia.org /wiki/Protein_sequencer (107 words)

	Methods (Site not responding. Last check: 2007-11-05)
		They are usually grown by the "hanging drop method" which means equilibrating a protein/ precipitant solution against a reservoir so that the concentration of the protein and the precipitants increases slowly.
		Methods for DNA analysis are sequencing, restriction fragment length polymorphism (RFLP), single strand conformation polymorphism (SSCP), protein truncation test (PTT) and heteroduplex analysis.
		The purified proteins from bacteria can both structurally be analyzed by X-ray crystallography or functionally be characterized by biophysical methods.
	www.mpi-dortmund.mpg.de /departments/dep1/methoden/methoden.php3 (2054 words)

	C-Reactive Protein (Site not responding. Last check: 2007-11-05)
		A two-site immunoradiometric assay for C-reactive protein in serum.
		METHODS:: A robust new polyclonal-monoclonal solid- phase IRMA for CRP was developed, with a range of 0.05-10.0 mg/L. RESULTS:: Plasma CRP values in general adult populations from Augsburg, Germany (2291 males and 2203 females; ages, 25-74 years) and Glasgow, Scotland (604 males and 650 females; ages, 25-64 years) were very similar.
		METHODS: C-reactive protein and LDL cholesterol were measured at base line in 27,939 apparently healthy American women, who were then followed for a mean of eight years for the occurrence of myocardial infarction, ischemic stroke, coronary revascularization, or death from cardiovascular causes.
	www.thedoctorsdoctor.com /labtests/crp.htm (6123 words)

	The Protein Disease Database of human body fluids: I
		In a study of lymphocyte proteins from Lesch-Nyhan patients, conducted soon after the introduction of 2-DE, it became apparent that numerous proteins might be affected even in diseases caused by a single gene mutation.
		Once proteins are resolved by methods such as electrophoresis, some of these proteins, such as hemoglobin, may be detected by their absorption of visible light.
		This class of proteins, first discovered in the laboratory of Avery in patients suffering from pneumococcal pneumonia (Abernathy and Avery, 1941), are generally defined as those whose concentrations increase or decrease by 25% or more in response to inflammation (Kushner, 1982; Kushner and Mackiewicz, 1993).
	www-lmmb.ncifcrf.gov /PDD/pdd-I.html (4129 words)

	B-114 PROTEIN DRUGS: MANUFACTURING TECHNOLOGIES (Site not responding. Last check: 2007-11-05)
		The main contributions of this study are the estimation of individual bulk protein quantities and their grouping by principal manufacturing methods.
		Excluded from consideration in this study are the methods and quantities of proteins produced for laboratory use, the methods and quantities of proteins produced for clinical trials, the methods and quantities of proteins for in vitro diagnostic use and the methods and quantities of proteins for in vivo diagnostic use.
		Proteins for veterinary use, their methods of production and quantities are excluded also, as are protein methods and quantities for other applications.
	www.bccresearch.com /biotech/B114.html (1402 words)

	Commonly Used Protein Assay Methods (Site not responding. Last check: 2007-11-05)
		There is no absolute method for determing the protein concentration when you have a mixture of proteins in a solution (see part 5 for discussion of pure proteins).
		By using a commonly available purified protein, it is easy for you and others to reproduce the results you obtain.
		Biuret - This method is the most linear because its color depends on a direct complex between the peptide bonds of the protein and Cu(2+) ion.
	www.bio.mtu.edu /campbell/Protein2.htm (433 words)

	E0046: Computational Protein Deisgn: Methods and Applications (Site not responding. Last check: 2007-11-05)
		Complete, de novo, sequence designs for small protein domains are now tractable, which allows for a critical evaluation of the physical-chemical basis of stability in proteins.
		That is, various potential energy functions that capture different aspects of protein stability and fold specificity can be explored in an effort to elucidate the origins of stability and specificity in naturally occurring proteins.
		In addition, the recent use of a computational protein design procedure to design a “protozyme” foreshadows the use of design procedures to evaluate the origins and evolution of enzymatic catalysis.
	www.hwi.buffalo.edu /ACA/ACA02/abstracts/text/E0046.html (152 words)

	Evaluation of Four Automated High-Sensitivity C-Reactive Protein Methods: Implications for Clinical and Epidemiological ...
		Regression analysis for the BN II method (A) gave a slope of 9.87, an intercept of 0.42, and an r of 0.997.
		For the IMx method (B), the slope was 13.33, the intercept was 0.48, and r was 0.997.
		For the IMMULITE method (C), the slope was 8.86, the intercept was 0.84, and r was 1.000.
	www.clinchem.org /cgi/content/full/46/4/461 (4267 words)

	Protein Methods#1
		If you measure A280 of the protein solution in an 1 cm cuvette, the value of e is ODs of 1 M solution.
		Basic procedure for purification of native proteins with His-tag.
		Purification of His-tag proteins with Ni-resins is very effective and fast way to get pure and active polypeptides, but you need to play first with different conditions of washing and elution for really good results.
	www.uhmc.sunysb.edu /bioscience/methods/protein_methods/protein_methods01.htm (428 words)

	Thesis: Chapter 2 - Protein crystallographic methods
		Thus the Patterson map of a protein would contain a large number of peaks, many of which coincide or overlap, since the width of a Patterson peak is the sum of the widths of the appropriate two peaks in the corresponding electron density maps.
		In protein crystallography, however, the data usually exhibit a certain degree of redundancy, which means that a statistically relevant number of data may be omitted from the data prior to refinement.
		In principle the starting point of CDM and entropy/likelihood methods is the same, but the latter do not require a uniform distribution of the probability distribution of the atoms in the asymmetric unit [Bricogne and Gilmore, 1990].
	www.ysbl.york.ac.uk /~mgwt/thesis-tth/chapter2.html (10865 words)

	Amazon.com: Protein Methods: Books: Daniel M. Bollag,Michael D. Rozycki,Stuart J. Edelstein (Site not responding. Last check: 2007-11-05)
		This revised and expanded Second Edition of Protein Methods remains the first source for a complete summary of tested and proven protein techniques.
		The chapter on protein isolation includes a new section focusing on the isolation of proteins from inclusion bodies.
		In the second section, four new chapters are devoted to protein purification and crystallization.
	www.amazon.com /exec/obidos/tg/detail/-/0471118370?v=glance (1256 words)

	Randomness in the Primary Structure of Protein: Methods and Implications (Site not responding. Last check: 2007-11-05)
		Randomness in the Primary Structure of Protein: Methods and Implications
		It is no doubt that the evolutionary process is affected by chance, but the question is to what extent the chance plays its role.
		With the use of random principles, we have explored three approaches to analyse protein primary structure, i.e.
	www.horizonpress.com /mbt/abstracts/v3/08.html (144 words)

	Protein Methods
		Separation methods A. Properties that are used to separate proteins: i.
		salting in versus salting out solubility of a protein close to its pI versus the effect of salt interacting with solvent and not the protein ii.
		ultracentrifugation B. Concentrating protein helps to maintain active protein sometimes addition of a carrier protein may help addition of glycerol C. Inhibitors i.
	www.siumed.edu /~bbartholomew/course_material/protein_methods.htm (320 words)

	Comparability of protein characterisation methods
		This short project reviewed the physico-chemical methods that are used to characterise proteins, with a particular emphasis on those techniques that can provide information about protein structure.
		Results from different organisations were so different that comparison of the data would predict that different proteins had been used in the study.
		Since UV-Vis absorbance is used as the gold standard for protein concentration measurement, the large difference observed between data sets would lead to significant differences in measured protein concentration.
	www.npl.co.uk /biotech/compare.html (366 words)

	Information Directory protein purification methods (Site not responding. Last check: 2007-11-05)
		and sensitivity in the purification of membrane proteins in the separation of...
		for protein purification but that each protein has unique...
		Protein Purification: Principles, High-Resolution Methods, and Applications, 2nd...
	www.healthy-shopper.com /protein/protein-purification-methods.htm (299 words)

	Mathematical Methods for Protein Structure Analysis and Design 2003 (Site not responding. Last check: 2007-11-05)
		Concettina Guerra, Sorin Istrail (Eds.): Mathematical Methods for Protein Structure Analysis and Design, Advanced Lectures.
		A Comparison of Methods for Assessing the Structural Similarity of Proteins.
		Prediction of Protein Secondary Structure at High Accuracy Using a Combination of Many Neural Networks.
	www.informatik.uni-trier.de /~ley/db/conf/msps/msps2003.html (187 words)

	B-114R Protein Drugs: Manufacturing Technologies (Site not responding. Last check: 2007-11-05)
		While this study provides discussion of post-bulk production operations, and data on formulation volumes and excipients for protein drugs, we do not go into detail on post-bulk production.
		This study estimates worldwide bulk drug protein production in grams for 1999 and forecasts the worldwide bulk production to 2004.
		Protein Drugs Made by Natural Plant Source Extraction
	www.bccresearch.com /biotech/B114R.html (2982 words)

	Protein Chemistry Methods and Protocols (Site not responding. Last check: 2007-11-05)
		Electroelution of Proteins From SDS-PAGE Gels (Mike A. Dyer, Harvard Medical School)
		Expression and Purification of His Tagged Proteins in E.
		Protein Gel Preparation and Staining (Mike A. Dyer, Harvard Medical School)
	www.ihcworld.com /neuroscience/protein_chemistry.htm (190 words)

	Acrylamide gel protein detection methods
		Top / Proteomics and protein biochemistry / In gel protein staining and digestion
		Brief protocols for acrylamide gel protein detection methods including coomassie blue R-250, G-250, silver staining, fluorescent detection and Ruthenium II method.
		Share your In gel protein staining and digestion related experience in discussion forum
	www.biowww.net /detail-874.html (73 words)

	Amazon.co.uk: Protein Methods: Books (Site not responding. Last check: 2007-11-05)
		RS Locums is a specialist agency with international experience in recruitment and is dedicated to finding employment for locum and permanent staff.
		Step-by-step protocols for the isolation, extraction, and application of proteins.
		This book includes new and updated procedures and complete lists of reagents and equipment.
	www.amazon.co.uk /exec/obidos/ASIN/0471118370 (365 words)

	P6308 Protein Methods 2nd ed.
		Revised and expanded, this edition remains the key source for tested and proven techniques.
		Four new chapters are devoted to protein purification by ion exchange, gel filtration, and affinity chromatography, and to protein crystallization.
		Use of this web site constitutes your acceptance of the Site Use Terms
	www.sigmaaldrich.com /catalog/search/ProductDetail?ProdNo=P6308&Brand=SIGMA (70 words)

	BioChemWeb.org Discussion Board :: View Forum - Protein Methods
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	www.biochemweb.org /discussion/viewforum.php?f=4 (86 words)

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