Question

1) What is one method that researchers can use to find the structure of protein with atomic level resolution? Also mention its primary strengths and weakness.

2) Describe (in detail) an α helix or a β sheet.

3) What functional groups are on Lys-Arg-Glu and what is the pI?

4) As a biochemist, what is the value of using proteases like trypsin?

Answer 1

ANSWER:-1 For this method, the protein is purified and crystallized, then subjected to an intense beam of X-rays. The proteins in the crystal diffract the X-ray beam into one or another characteristic pattern of spots, which are then analyzed (with some tricky methods to determine the phase of the X-ray wave in each spot) to determine the distribution of electrons in the protein. The resulting map of the electron density is then interpreted to determine the location of each atom.The coordinate files include atomic positions for the final model of the structure, and the data files include the structure factors (the intensity and phase of the X-ray spots in the diffraction pattern) from the structure determination. You can create an image of the electron density map using tools like the Astex viewer, which is available through a link on the Structure Summary page.

X-ray crystallography can provide very detailed atomic information, showing every atom in a protein or nucleic acid along with atomic details of ligands, inhibitors, ions, and other molecules that are incorporated into the crystal. However, the process of crystallization is difficult and can impose limitations on the types of proteins that may be studied by this method. For example, X-ray crystallography is an excellent method for determining the structures of rigid proteins that form nice, ordered crystals.

ANSWER:-2 Alpha helices and β pleated sheets are the secondary structure of polypeptides. Each occurs as a result of various arrangements of hydrogen bonds between the residues contained therein.To be sure, α helices are twisted and β pleated sheets are two sheets of the polypeptide chain from it bending once at the top and interacting.

ANSWER 3:-The functional groups on Lys-Arg-Glu are alpha-COOH, alpha-NH3.

ANSWER:-4Trypsin present in higher animals has very little sequence identity with microbial trypsins, but all trypsins are similar structurally. In particular, Streptomyces griseus trypsin has a very similar fold to these proteases [60]. Other microbial proteases are more distantly related, having shorter amino acid sequences and corresponding surface loops. For instance, α-lytic protease has the same fold as trypsin, but differs greatly in many structural aspects [61]. Many other serine proteases such as the kallikreins, elastase and chymotrypsin comprise the trypsin family and these are very similar structurally and mechanistically to trypsin, but differ in other key aspects such as substrate preferences and overall biological function.