Showing papers in "Methods of Molecular Biology in 1994"
TL;DR: A rapid and accurate method for the estimation of protein concentration is essential in many fields of protein study, but is susceptible to interference from a wide range of compounds commonly present in biological extracts.
Abstract: A rapid and accurate method for the estimation of protein concentration is essential in many fields of protein study. The Lowry method ( Chapter 1 in vol. 1 of this series) has been widely used, but is susceptible to interference from a wide range of compounds commonly present in biological extracts. Although interference can be avoided by trichloracetic acid precipitation of the protein prior to assay, this lengthens the procedure.
1,573 citations
TL;DR: Using the FASTA Program to Search Protein and DNA Sequence Databases, and Converting Between Sequence Formats.
Abstract: GCG: Fragment Assembly Programs. GCG: Drawing Linear Restriction Maps. GCG: Drawing Circular Restriction Maps. GCG: Displaying Restriction Sites and Possible Translations in a DNA Sequence. GCG: Assembly of Sequences into New Sequence Constructs. GCG: Comparison of Sequences. GCG: Production of Multiple-Sequence Alignment. GCG: Database Searching. GCG: Pattern Recognition. GCG: Translation of DNA Sequence. GCG: Analysis of Protein Sequences. GCG: The Analysis of RNA Secondary Structure. GCG: Preparing Sequence Data for Publication. MicroGenie: Introduction and Restriction Enzyme Analysis. MicroGenie: Shotgun DNA Sequencing. MicroGenie: Translation. MicroGenie: Protein Analysis. MicroGenie: Homology Searches. PC/GENE: Sequence Entry and Assembly. PC/GENE: Restriction Enzyme Analysis. PC/GENE: Translation and Searches for Protein Coding Regions. PC/GENE: Sequence Comparisons and Homologies. PC/GENE: Database Searches. PC/GENE: Searches for Functional Sites in Nucleic Acids and Proteins. Using the FASTA Program to Search Protein and DNA Sequence Databases. Converting Between Sequence Formats. Obtaining Software via INTERNET. Submission of Nucleotide Sequence Data to EMBL/GenBank/DDBJ. Index.
1,106 citations
579 citations
346 citations
308 citations
248 citations
TL;DR: Lowry protein estimations are a completely acceptable alternative to a rigorous absolute determination in almost all circumstances where protein mixtures or crude extracts are involved.
Abstract: The most accurate method of determining protein concentration is probably acid hydrolysis followed by amino acid analysis. Most other methods are sensitive to the amino acid composition of the protein and absolute concentrations cannot be obtained. The procedure of Lowry et al. (1) is no exception, but its sensitivity is moderately constant from protein to protein, and it has been so widely used that Lowry protein estimations are a completely acceptable alternative to a rigorous absolute determination in almost all circumstances where protein mixtures or crude extracts are involved.
242 citations
TL;DR: The methods discussed here are those used frequently in primary structure analysis and in the identification of essential groups involved in the binding and catalytic sites of proteins.
Abstract: The two most widely used applications for chemical modification are in primary structure analysis and in the identification of essential groups involved in the binding and catalytic sites of proteins. The methods discussed here are those used frequently in primary structure analysis. Chemical modifications involving protein "active center" identification are the subject of a review by Pfleiderer (1).
220 citations
209 citations
158 citations
TL;DR: In this article, the authors present general forms of the equations required to extract thermodynamic data from equilibrium transition curves on oligomeric and polymeric nucleic acids of any molecularity.
Abstract: Publisher Summary This chapter presents general forms of the equations required to extract thermodynamic data from equilibrium transition curves on oligomeric and polymeric nucleic acids of any molecularity. The reason that the equations and protocols are general, they also can be used to characterize thermodynamically equilibrium processes in systems other than nucleic acids. This work reviews how the reduced forms of the general equations have been used by many investigators to evaluate mono-and bimolecular transitions and then explains how these equations can be generalized to calculate thermodynamic parameters from common experimental observables for transitions of higher molecutarities. The strengths and weaknesses of each method of data analysis are emphasized, so that investigators can select the approach most appropriate for their experimental circumstances. This work also describes how to analyze calorimetric heat capacity curves and non-calorimetric differentiated melting curves to extract both model-independent and model-dependent thermodynamic data for transitions of any molecularity. The general equations and methods of analysis described should be of that are investigating association and dissociation processes in nucleic acids that exhibit molecularities greater than 2.
TL;DR: The O'Farrell 2-D gel system has no serious rivals and therefore, with the modification of non-equilibrium pH-gradient electrophoresis (NEPHGE) to analyze basic proteins, almost any polypeptide may be investigated.
Abstract: Since O'Farrell (1) introduced the improved technique for high resolution two-dimensional polyacrylamide gel electrophoresis (2-D PAGE), it has become one of the most powerful tools for the separation and quantification of proteins from complex mixtures. The principal reason for this is that the method employs separation of denatured proteins according to two different parameters, molecular weight and isoelectric point. Consequently, it has sufficient resolution to separate individual proteins as discrete spots on the gel. Each parameter may also be varied and therefore, with the modification of non-equilibrium pH-gradient electrophoresis (NEPHGE) to analyze basic proteins (2), almost any polypeptide may be investigated. Thus to date, the O'Farrell 2-D gel system has no serious rivals, with the possible exception of the Kaltschmidt and Wittmann (3) gel system for analyzing ribosomal proteins. Ribosomal proteins, however, may be adequately separated with NEPHGE.