Assignment #2    Aspects of Protein Structure

Due date: Thursday September 20, 2001 
[Turn in at beginning of class period.]
You may work in pairs on this assignment.  If so, be sure
to indicate both members of the pair when submitting your work.

Objective:  This exercise is designed to introduce you to aspects of 
protein structure and to a research tool available to researchers and 
students alike for investigating  protein models.  [There will be some 
limitations due to computer access.]

Background:  When compared to lipids and carbohydrates, we are amazed at 
the enormous structural diversity displayed by proteins.  One can 
generalize that the typical protein contains, on average, 500 amino 
acids (residues).   In the primary structure, any of the 20 amino  acids 
may be at any of the 500 positions, a mind-boggling number of 
possibilities.
The interactions of the amino acids with their neighbors then determines 
secondary structure, etc.  The resulting folding of the molecule conveys 
a native conformation which may be examined with techniques such as NMR
and X-ray diffraction, enabling researchers to hypothesize molecular 
structure.  This information is submitted to databases for dissemination. 

In this exercise you will utilize information about several proteins, 
provided by such a database and your text, to investigate protein 
structure.  There are 4 problems to address.  Directions are given
below; questions are on the response sheet.

Preparation:  Study/review the discussion of protein structure in 
Chapter 3.  You will need the following specific information to complete
the exercise: Table 3-2; Fig. 3-2 and 3-8
 

Please use and submit the Assignment #2 RESPONSE Sheet:

Print the sheet by clicking on the "File" menu at the top of the
browser; select "Print".        
Return to this page by clicking the "Back" button.

Problems are presented below with appropriate links.

Proceed below. Read the info for the problem before linking.
(You may wish to print the information below to simplify)
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

Problem #1

Text Figure 3-11 [pg 53].  Examine the figure of the 3-D structure of 
ribonuclease and answer the questions on the Response Sheet.

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Problem #2

 Link to Protein Database 
to view the comments about and the space-filling model of Myoglobin. 
Answer questions 1 and 2 on the Response Sheet.

Link to the specific information on this protein by clicking on the code 
1mbn  while on the myoglobin page.  
This link connects you to the summary page for myoglobin in the Protein 
Data Bank.
The original citation is given as well as other information concerning the 
molecule.
   For example - the HET group is identified as having a heme group.
BELOW you will find some other information about the site.
At the left of the screen there is a blue menu.  Click on Sequence Details 
and use info from that screen to answer questions 3 - 5.   You may certainly
try other links on the menu but not all of the computers on campus will load
other information (and may be time consuming). "View Structure" will not 
load unless you have one of the imaging tools loaded.  However, there is 
usually a small image at the upper right-hand corner of the page.

In the OVERVIEW section, information is presented about the specific 
molecule or the portion that is being analysed.  For example:

Chains	Residues	Mol. Weight [D]	  Chain Type
1AB1:_	  46      	    4709	    Protein

All entries include the following final set of data items:
·	Polymer Chains: lists the chain identifiers for all chains in the 
structure entry. 
·	Residues: gives the number of amino acids (for proteins) or bases 
(for nucleic acids) contained in the entry. 
·	Atoms: gives the number of non-hydrogen atoms contained in the 
structure entry. This count includes waters and ligands. Atoms which are 
described in terms of discrete disorder (multiple sites) are counted once. 
·	HET groups: lists the three letter codes that identify het groups 
(typically, water molecules, bound ions and ligands) in the structure 
entry. The het group ids have no special significance. The chemical names 
are typically common names where there is widespread usage. Otherwise 
systematic names have been used. 
Sequence Details: The sequence of each chain is reported for the selected 
structure. The display includes the molecular weight in kiloDaltons (kD). 
The molecular weight is calculated based on the amino acid sequence over 
the standard residue types - bound ligands and residue modifications are 
not included. Each residue in the sequence is reported as a single letter 
code. Secondary structure is calculated and described according to an 
implementation of the method of Kabsch and Sander (1983) Biopolymers 22, 
2577-2637. The assignments are: H=helix; B=residue in isolated beta 
bridge; E=extended beta strand; G=310 helix; I=pi helix; T=hydrogen bonded 
turn; S=bend.

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Problem # 3


 Link to Protein Database 
to view the comments about and the space-filling model of Pepsin. 
Answer questions 1 and 2 on the Response Sheet.

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Problem # 4

 Link to Protein Database 
to view the comments about and the space-filling model of Alcohol 
dehydrogenase. 
Then link to PDB entry 1agn (2nd paragraph)  and the Sequence Details pg.
Answer questions 1 and 2 on the Response Sheet.



SOURCE:
"The Research Collaboratory for Structural Bioinformatics (RCSB) is a 
non-profit consortium dedicated to improving our understanding of the function of 
biological systems through the study of the 3-D structure of biological 
macromolecules."  This service is maintained by Rutgers University.