17 Aug Question: Use Swiss PDBViewer (or Your Favorite Structure Viewer) To Analyze The Structures And Answer The Following Questions. Classify The Folds Of The Following Proteins. (Each Is A Single Domain. If There Is More Than One Chain Or Model, Only Examine One.) For Each Domain, Classify The Fold As All A (or Mostly A), All B (or Mostly B), A/b, Or A+b. +2 Each …

Use Swiss PDBViewer (or your favorite structure viewer) to analyze the structures and answer the following questions.

1. Classify the folds of the following proteins. (Each is a single domain. If there is more than one chain or model, only examine one.) For each domain, classify the fold as
   all a (or mostly a), all b (or mostly b), a/b, or a+b.       +2 each
   1. Pyrococcus nucleotide triphosphate pyrophosphatase (1PNP)
   2. Rhodobacterial membrane protease (2RMP; ignore chain B, which is an inhibitor)
   3. Human galactose-binding protein (3GBP; load 1 model)
2. Examine the following proteins and determine how many domains each polypeptide has. (If there is more than one chain or model, only examine one.) List the residues in each domain (e.g. 17-98, 141-169), and classify each domain (as in part 1).            +2 each
   1. Streptococcal trans-sialidase (4STS)
   2. Simian sentinel cell receptor (5SSR)
   3. Human thyroxine-binding protein (6TBP)
3. Examine the following multimeric proteins and classify the symmetrical arrangement of the subunits (e.g. C₂, C₃, D₂, helical, icosahedral). If the program asks you to “Load __ models”, just hit OK with whatever number it has by default. (Note that each model will load as a different layer.)                        +2 each
   1. Human thyroxine-binding protein (6TBP)
   2. Gorilla xylulokinase (7GXK)
   3. Firmicute isopentenyl pyrophosphate isomerase (8FIP)

4. Examine the 2 pairs of proteins below. In each case, these are enzymes that catalyze the same reaction in different species. The question is: are they related or not? i.e. Are the structures essentially the same? Often you can get similar reactions from proteins that evolved from a common ancestor (e.g. trypsin and chymotrypsin). Sometimes the same reaction can be catalyzed by proteins with very different evolutionary origins and with very different structures (e.g. trypsin and subtilisin). Your job is to decide if these proteins have fundamentally different folds or if they have basically the same fold. Briefly justify your answer (≤3 sentences).              +3 each
   1. Firmicute and Archaeal isopentenyl pyrophosphate isomerase (8FIP & 9PIP)

2. Archaeal and Proteobacterial 3-dehydroshikimate hydratase (10ADH & 11PDH)

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