What information can you gather from sequence alignments such as these? b. Based

Question

What information can you gather from sequence alignments such as these?
b. Based on this sequence alignment, can you predict if the proteins will exhibit
structural and functional similarity with each other? If your answer is yes, then
justify how you arrived at this conclusion. If your answer is no, then describe what
other information you would need to possibly make a decision.
c. You are interested in determining the active site residues of these proteins and
propose to carry out single amino acid mutations. Which amino acids would you
select for mutation? Why did you select these particular amino acids?
d. After you have expressed and purified the single amino acid mutants your boss
suggests that you should verify the overall secondary structure of the protein is
similar to that of the wild type protein. Do you agree with this suggestion? Why
or why not.

Shown below is the sequence alignment for five proteins that are thought to
function as amidohydrolases”. The proteins aligned are as follows:
Row 1 - Agrobacterium Dcase; Row 2 - Pseudomonas Dcase; Row 3 - P. aeruginosa
amidase; Row 4 - C. testosteroni nitrilase; Row 5 - rat b-alanine synthase

B1 B2 o2 10 20 30 40 50 60 DMLT WHFTDEAELDS 66 TROMILAVGQQG TRE ASR. TTFFPR. 66 TRI AAAAOMG EAKAR DL TTFFPR. WYWIEDEAELDS 3 MRHGDIE SSSNDT IADMI GMROGLPG MKNYPT FMUNLEAA IAE ASME IMYDPALEMME 74 DL SLOG PG-YPYWIWTSN MDFTGMMWA 70 5 AAKEQORCPOIVRVGLVONRIPLPTSAPM--AEQVSALH FAFcTREKLPWT 76 AMC II B3 B5 cu4 70 80 90 100 110 120 130 140 EMPG PvVRPLFE GENIGYA-ELVVEGGVKRRENTS iRSGK 149 YET-E ELGI ILV Di IV OHL EIGFYLGYA-ELAEEGGRKRRi VHL GHKEPOPGRKHQH ILVDE 149 PETOPLFDE 145 TAVE IP EETEIFSRAC IDI CPI PNGN HRKF-KP----------- TSS 140 VLFKNAIE IP SKEVQQISD 5 E-EAES-AED LTTRFCOKL SPIL-ERDRDHG-G 151 SNS HI PRVG DF ST B6 B7 a5 B8 160 170 180 190 200 210 220 EpGD-LGFP DvDAAKMGM FICNDRRWPE TETHNPPvPOHDHLTSF HHLLSMQAGSYON GYN 226 CG. 226 EP LGFG RAF DGVMGMC CNDRR ET GYN DHTGHDDIDSLTOFHNHLSMOAGAYON DOovMMAKAMAWANNCYVAVANAAG; FDGVY 227 PGG-OTYVSEGPRAGM KISLIICDDGNYPEI GD SMAP TEHALPILNIAAMGSLNEOVIHVA-SWPAF 5 ME CYGRHHPLN NLMYSMNG QEH 233 B9 B10 B11 B12 B13 B14 a8 230 240 250 260 270 280 290 IVALTTTLEDEVITAAvDILDRCREL HIFNFROHROPOH 296 HSC APTG STWVIGTAKCGTEEGSKMVGOSVIVAP SYFGH SAIIGFDGRTLGEC 5 YPNEFTSG KAHHDLGYF ss YvAAPDGsRTPGLSRNO ----DGLLVTELNLNL CQQINDFWTF KMTGRLEMYARELAEAVKPN 316 300 YGLIAEL 303 2 YRLIVERKGAVPPPO 311 3 EKARDNVERL TRSTTGVAQCPVGRLPYEGLEKEA 346 OSEHV PVKKI GEQTNHFISYEDLHED KMDMLTI PPRRIVATA 354 333 5 YSPNIVKEDLVLAP SSG Structur

Explanation / Answer

Answer:

Based on the above sequence alignment, we can predict that the proteins will exhibit structural and functional similarity with each other because the above proteins have identical amino acid residue sequences. These proteins might be evolved from the common ancestor.

For determining the active site residues of these proteins, we should select the identical amino acid residues because of the similar structure or function.

After expression in suitable host and purification of single amino acid mutants, we should verify the overall secondary structure of the protein with wild-type protein because mutated protein not supposed to disturb the overall secondary structure of the protein

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