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Mascot identifies proteins by interpreting mass spectrometry data. The prevailing experimental method for protein identification is a bottom-up approach, where a protein sample is typically digested with trypsin to form smaller peptides. While most proteins are too large, peptides usually fall within the limited mass range that a typical mass ...
Ribbon diagrams, also known as Richardson diagrams, are 3D schematic representations of protein structure and are one of the most common methods of protein depiction used today. The ribbon depicts the general course and organization of the protein backbone in 3D and serves as a visual framework for hanging details of the entire atomic structure ...
Protein dynamics and conformational changes allow proteins to function as nanoscale biological machines within cells, often in the form of multi-protein complexes. [14] Examples include motor proteins, such as myosin, which is responsible for muscle contraction, kinesin, which moves cargo inside cells away from the nucleus along microtubules ...
Proteins are primarily classified by sequence and structure, although other classifications are commonly used. Especially for enzymes the EC number system provides a functional classification scheme. [31] Similarly, gene ontology classifies both genes and proteins by their biological and biochemical function, and by their intracellular location ...
The software evaluates protein sequences from a database to compute the list of peptides that could result from each. The peptide's intact mass is known from the mass spectrum, and Sequest uses this information to determine the set of candidate peptides sequences that could meaningfully be compared to the spectrum by including only those near ...
At the top level are all alpha proteins (domains consisting of alpha helices), all beta proteins (domains consisting of beta sheets), and mixed alpha helix/beta sheet proteins. While most proteins adopt a single stable fold, a few proteins can rapidly interconvert between one or more folds. These are referred to as metamorphic proteins. [5]
These methods determined the mass of peptides using mass spectrometry, and then used the mass to search protein databases to identify the proteins [3] [4] In 1999 a more complex program was released called Mascot that integrated three types of protein/database searches: peptide molecular weights, tandem mass spectrometry from one or more ...
A simpler method for analysis of bound ligands uses a protein precipitation extraction to denature proteins and release ligands into the precipitation solution, which can then be diluted and identified on an LC-MS system. An example target identification by chromatographic co-elution (TICC) workflow.