asinment30 by SBMirza


                           S B Mirza 1314

        Tehseen Gulzar



                                     Proteomics Questions

Question #1:

Yes conformational variations are responsible for differences in the 3d structure of
protein.Most proteins fold into unique 3-dimensional structures. Although many proteins can fold
unassisted, simply through the chemical properties of their amino acids, others require the aid of
molecular chaperones to fold into their native states.

Proteins are not entirely rigid molecules. proteins may shift between several related structures while
they perform their functions. In the context of these functional rearrangements, these tertiary or
quaternary structures are usually referred to as "conformations", and transitions between them are
called conformational changes. Such changes are often induced by the binding of a substrate molecule
to an enzyme's active site, or the physical region of the protein that participates in chemical catalysis. In
solution proteins also undergo variation in structure through thermal vibration and the collision with
other molecules

Question #2:

       Secondary structure
           o 1.2 Chou-Fasman method
           o 1.3 GOR method
           o 1.4 Machine learning
           o 1.5 Other improvements
       Tertiary structure
           o 2.1 Ab initio protein modelling
           o 2.2 Comparative protein modelling
           o 2.3 Side chain geometry prediction
           o 2.4 Prediction of structural classes
       Quaternary structure
            o   protein–protein docking
       Automatic structure prediction servers
            o   MODELLER
            o   I-TASSER
            o   RAPTOR

Question #3:

Protein mass spectrometry refers to the application of mass spectrometry to the study of proteins. Mass
spectrometry is an important emerging method for the characterization of proteins. The two primary
methods for ionization of whole proteins are electrospray ionization (ESI) and matrix-assisted laser
desorption/ionization (MALDI). In keeping with the performance and mass range of available mass
spectrometers, two approaches are used for characterizing proteins. In the first, intact proteins are
ionized by either of the two techniques described above, and then introduced to a mass analyzer. This
approach is referred to as "top-down" strategy of protein analysis. In the second, proteins are
enzymatically digested into smaller peptides using a protease such as trypsin. Subsequently these
peptides are introduced into the mass spectrometer and identified by peptide mass fingerprinting or
tandem mass spectrometry. Hence, this latter approach (also called "bottom-up" proteomics) uses
identification at the peptide level to infer the existence of proteins.

S b mirza1314                                                                                         Page 1

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