Question

List and describe the two approaches to determining the tertiary structure of a protein. Experimental Determination Computational prediction There are three methods of computational structure prediction. Define each of the methods and describe when each method would be used. There are three types of helices formed by the secondary structure of protein. List three helices and rate how tightly coiled they are. Explain your reasoning. Choose any three of the twenty amino acids. Based on what you know about the properties of the amino acids describe where in the final structure the amino acid would most likely be. Justify your answer.

Answer 1

8. a) EXPERIMENTAL DETERMINATION:
The structure of hemoglobin at 6 Å and demonstrated that the folding of the globin chain is similar to that in myoglobin, despite relatively low sequence homology between the two. This observation of a family pattern to the three-dimensional structure of globins has been followed by the identification of many other families.
Today, several hundred proteins have been analyzed by x-ray diffraction and their three-dimensional structures catalogued. This number continues to grow at an ever-increasing rate and, together with the amino acid and gene sequence data, forms the principal basis for understanding the mechanisms of action of these proteins at the molecular level.
b) COMPUTATIONAL PREDICTION:
At present, modern crystallography depends completely on heavy computer use, and this dependence will certainly increase steadily in the future. In the four mathematical procedures required to solve a structure using protein crystallography—data processing, phase determination, map fitting, and refinement—new methods are continually appearing that depend on ready access to considerable computer power.
Molecular replacement techniques have also been applied in the use of redundancy to obtain phase information. A spectacular illustration of this occurred in the recent analyses of the picornaviruses for polio and the common cold.
These methods require heavy computational analysis for their success.
9. These methods can be divided in three main classes:
(a) first principle methods without database information;
(b) fold recognition and threading methods;
(c) comparative modeling methods and sequence alignment strategies.
10. (1) the chain of amino acids will continually twist around in a helical formation (something like the telephone cord) and stay twisted due to the presence of the hydrogen bonds. This helix is known as an alpha-helix. Every amino acid can form a peptide bond and therefore one might assume that every amino acid can form an apha-helix (note that R-groups are not involved in the hydrogen bonding that holds the helix together). In nature, however, several amino acids do not "fit" well into an due to either the size of the R- groups (large R-groups prevent the chain from twisting) or to the charge of the R-groups (charged R-groups want to form ionic bonds [which are stronger than hydrogen bonds] with other oppositely charged R-groups which pulls the chain away from the helix structure). This means that while some amino acids "like" to form helices, others don't. If one knows the primary sequence of a peptide chain, one could predict which areas of the chain would most likely form a helix and which areas don't based upon the amino acid sequence of those regions.
(2)The beta-sheet likewise is held together by hydrogen bonds but generally only areas that contain large amounts of the amino acid glycine like to form these sheets.
11. (1) Glycine: The amino acid glycine does not have a side chain and is hard to assign to one of the above classes. However, glycine is often found at the surface of proteins, often within loops, providing high flexibility to these regions.

(2) Proline: Proline has the opposite effect, providing rigidity to the protein structure by imposing certain torsion angles on the segment of the polypeptide chain. The reason for these effects is discussed in the section on torsion angles. These two residues are often highly conserved in protein families since they are essential for preserving a particular protein three-dimensional fold.
(3) Alanine: Most protein molecules have a hydrophobic core, which is not accessible to solvent and a polar surface in contact with the environment (although membrane proteins follow a different pattern). While hydrophobic amino acid residues build up the core, polar and charged amino acids preferentially cover the surface of the molecule and are in contact with solvent due to their ability to form hydrogen bonds (by donating or accepting a proton from an electronegative atom).