1. Download a structure for one of the following proteins from the Protein Databank (the pdb code is in parentheses after each name). Use Rasmol or the Swiss PDB viewer to visualize the structure. Describe the types of secondary (helices, sheets) and tertiary structure (motifs, domains) that are present. Generate pictures that show clearly the kinds of features you identify.

2. The sequence below is that of a recombinant fungal lignin peroxidase, an enzyme that is one of the few things on the planet, short of a pulp mill, that can degrade lignin. Submit the sequence to the PsiPred server for prediction of its secondary structure. Retrieve the result as a pdf file, and attach it as your answer to this problem.

VIEKRATCSNGKTVGDASCCAWFDVLDDIQQNLFH
GGQCGAEAHESIRLVFHDSIAISPAMEAQGKFGGG
GADGSIMIFDDIETAFHPNIGLDEIVKLQKPFVQK
HGVTPGDFIAFAGAVALSNCPGAPQMNFFTGRAPA
TQPAPDGLVPEPFHTVDQIINRVNDAGEFDELELV
WMLSAHSVAAVNDVDPTVQGLPFDSTPGIFDSQFF
VETQLRGTAFPGSGGNQGEVESPLPGEIRIQSDHT
IARDSRTACEWQSFVNNQSKLVDDFQFIFLALTQL
GQDPNAMTDCSDVIPQSKPIPGNLPFSFFPAGKTI
KDVEQACAETPFPTLTTLPGPETSVQRIPPPPGAR
ATCSNGKTVGDASCCAWFDVLDDIQQNLFHGGQCG
AEAHESIRLVFHDSIAISPAMEAQGKFGGGGADGS
IMIFDDIETAFHPNIGLDEIVKLQKPFVQKHGVTP
GDFIAFAGAVALSNCPGAPQMNFFTGRAPATQPAP
DGLVPEPFHTVDQIINRVNDAGEFDELELVWMLSA
HSVAAVNDVDPTVQGLPFDSTPGIFDSQFFVETQL
RGTAFPGSGGNQGEVESPLPGEIRIQSDHTIARDS
RTACEWQSFVNNQSKLVDDFQFIFLALTQLGQDPN
AMTDCSDVIPQSKPIPGNLPFSFFPAGKTIKDVEQ
ACAETPFPTLTTLPGPETSVQRIPPPPGA

3. Download the pdb files for cytochrome C from tuna (5cyt) and rice (1ccr). Identify the residues (Rasmol?) that seem to be involved in binding the heme in each, and describe any differences. Then do an alignment of the sequences of the two proteins, and determine how many differences in sequence occur away from the heme binding site. Several investigators have suggested that evolution should produce variations most rapidly in regions of proteins that are least essential for their function. Do your observations agree with this generalization?

For preparing the alignment, you can use one of the tools available at the Expasy web site, ClustalW web site (where you can also download the software to your own PC), or download another alignment editor, such as GeneDoc. Be sure you indicate as part of your response how you prepared the alignment. I suggest the BLOSUM62 scoring matrix.

4. Below is the sequence of a human tumor antigen in FASTa format.

>P04637|P53_HUMAN Cellular tumor antigen p53 - Homo sapiens (Human).
MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGP
DEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAK
SVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHE
RCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNS
SCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELP
PGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPG
GSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD

Follow the steps in the tutorial to build a homology model of this protein. Save the output from the modeling as a .pdf file (use the button near the top of the output page) and submit that file as your answer to this question.

Please feel free to email me (rcfort@maine.edu) if you have any difficulties doing these problems.