Question

Met-Ala-Arg-Tyr-Ala-Asn-Asn-Glu__Lys-Glu-Leu-Leu-Tyr__Arg-Tyr-Ala-Asn__Phe-Leu-Ala-Asn-Asn-Ile-Gly-Ala-Asn__Ile-Ser__Ile-Asn-Thr-Glu-Arg-Glu-Ser-Thr-Glu-Asp__Ile-Asn__

His-Glu-Arg__Phe-Ala-Thr-His-Glu-Arg-Ser__Thr-Arg-Ile-Gly-Leu-Tyr-Cys-Glu-Arg-Ile-Asp-Glu__Leu-Glu-Val-Glu-Leu-Ser__Ser-Ile-Asn-Cys-Glu__His-Glu-__His-Ala-Pro-Pro-Ile-Leu-Tyr__Glu-Ala-Thr-Ser__Val-Ala-Asn-Ile-Leu-Leu-Ala__Cys-Ala-Lys-Glu-__Ala-Asn-Asp__Pro-Glu-Cys-Ala-Asn__Pro-Ile-Glu__Trp-Ile-Thr-His__Phe-Arg-Ile-Glu-Asp__Cys-His-Glu-Glu-Ser-Glu-Cys-Ala-Lys-Glu__Ile-Cys-Glu__Cys-Arg-Glu-Ala-Met__Glu-Val-Glu-Arg-Tyr-Asp-Ala-Tyr__Ala-Asn-Asp__Ser-His-Glu__Ile-Ser__Asp-Glu-Val-Ala-Ser-Thr-Ala-Thr-Glu-Asp__Thr-His-Ala-Thr__Asp-Ile-Ser-Glu-Ala-Ser-Glu-Ser__Leu-Ile-Lys-Glu__His-Glu-Ala-Arg-Thr__Asp-Ile-Ser-Glu-Ala-Ser-Glu__Ser-Leu-Glu-Glu-Pro__Ala-Pro-Asn-Glu-Ala__Ser-Glu-Val-Glu-Arg-Glu__Trp-Glu-Ile-Gly-His-Thr__Gly-Ala-Ile-Asn__Trp-Ile-Leu-Leu__Ala-Arg-Ile-Ser-Glu__Ile-Phe__His-Glu__Lys-Glu-Glu-Pro-Ser__Thr-His-Ile-Ser__Glu-Ala-Thr-Ile-Asn-Gly__Pro-Ala-Thr-Thr-Glu-Arg-Asn__Tyr-Glu-Thr__Ile-Phe__His-Glu__Trp-Trp-Trp-Trp-Ile-Ile-Ile-Ile-Ile-Leu-Leu-Leu-Leu-Leu-Ser-Ser-Ser-Ser__Cys-His-Ala-Asn-Gly-Glu__Ile-Asn__His-Ile-Ser__Leu-Ile-Phe-Glu-Ser-Thr-Tyr-Leu-Glu__His-Glu__Cys-Ala-Asn__Ser-Thr-Ile-Leu-Leu__Arg-Glu-Met-Ala-Ile-Asn__His-Glu-Ala-Leu-Thr-His-Tyr__Ser-Ala-Ser-Ser-Tyr__Ala-Asn-Asp__Ala-Leu-Arg-IleGly-His-Thr

1.) Write out the 1 letter amino acid abbreviation for each of the three-letter amino acid abbreviated words listed in the given sequence. The __ indicates a space in between the words.

Use www.expasy.org and other bioinformatic tools to generate the following bioinformatic data for the given polypeptide sequence. You must give the name and link to the program you used to generate the data:

2.) Compute the pI and Mw (isoelectric point and molecular mass, respectively) of the protein.

3.) Determine if and how many transmembrane regions does this protein have. If does than draw the orientation of with the N and C termini of the protein across the membrane.

4.) Determine the subcellular localization of this protein.

Need help with all parts 1-4 please and thank you

Answer 1

1. the one letter amino acid abbreviation for the sequence:

MARYANNE_LELLY_REAN_FLANNIGAN_IS_INTERESTED_IN_HER_FATHERS_TRIGLYCERIDE_LEVELS_SINCE_HE_HAPPILY_EATS_VANILLA_CAKE_AND_PECAN_PIE_WITH_FRIED_CHEESECAKE_ICE_CREAM_EVERYDAY_AND_SHE_IS_DEVASTATED_THAT_DISEASES_LIKE_HEART_DISEASE_SLEEP_APNEA_SEVERE_WEIGHT_GAIN_WILL_ARISE_IF_HE_KEEPS_THIS_EATING_PATTERN_YET_IF_HE_WWWWIIIIILLLLLSSSS_CHANGE_IN_HIS_LIFESTYLE_HE_CAN_STILL_REMAIN_HEALTHY_SASSY_AND_ALRIGHT

2. pI and MW computation for the given sequence by ExPASy ProtParan tool (Source: https://web.expasy.org/cgi-bin/protparam/protparam)

ProtParam

User-provided sequence:

        10         20         30         40         50         60 
MARYANNELE LLYREANFLA NNIGANISIN TERESTEDIN HERFATHERS TRIGLYCERI 

        70         80         90        100        110        120 
DELEVELSSI NCEHEHAPPI LYEATSVANI LLACAKEAND PECANPIEWI THFRIEDCHE 

       130        140        150        160        170        180 
ESECAKEICE CREAMEVERY DAYANDSHEI SDEVASTATE DTHATDISEA SESLIKEHEA 

       190        200        210        220        230        240 
RTDISEASES LEEPAPNEAS EVEREWEIGH TGAINWILLA RISEIFHEKE EPSTHISEAT 

       250        260        270        280        290        300 
INGPATTERN YETIFHEWWW WIIIIILLLL LSSSSCHANG EINHISLIFE STYLEHECAN 

       310        320        330 
STILLREMAI NHEALTHYSA SSYANDALRI GHT 

References and documentation are available.

Number of amino acids: 333 Molecular weight: 37883.59 Theoretical pI: 4.51

Amino acid composition:
Ala (A) 36 10.8% Arg (R) 16 4.8% Asn (N) 22 6.6% Asp (D) 11 3.3% Cys (C) 10 3.0% Gln (Q) 0 0.0% Glu (E) 57 17.1% Gly (G) 7 2.1% His (H) 19 5.7% Ile (I) 36 10.8% Leu (L) 25 7.5% Lys (K) 4 1.2% Met (M) 3 0.9% Phe (F) 6 1.8% Pro (P) 8 2.4% Ser (S) 30 9.0% Thr (T) 21 6.3% Trp (W) 7 2.1% Tyr (Y) 10 3.0% Val (V) 5 1.5% Pyl (O) 0 0.0% Sec (U) 0 0.0% (B) 0 0.0% (Z) 0 0.0% (X) 0 0.0%

Total number of negatively charged residues (Asp + Glu): 68 Total number of positively charged residues (Arg + Lys): 20 Atomic composition: Carbon C 1644 Hydrogen H 2522 Nitrogen N 452 Oxygen O 553 Sulfur S 13 Formula: C₁₆₄₄H₂₅₂₂N₄₅₂O₅₅₃S₁₃Total number of atoms: 5184 Extinction coefficients: Extinction coefficients are in units of M^-1 cm^-1, at 280 nm measured in water. Ext. coefficient 54025 Abs 0.1% (=1 g/l) 1.426, assuming all pairs of Cys residues form cystines Ext. coefficient 53400 Abs 0.1% (=1 g/l) 1.410, assuming all Cys residues are reduced Estimated half-life: The N-terminal of the sequence considered is M (Met). The estimated half-life is: 30 hours (mammalian reticulocytes, in vitro). >20 hours (yeast, in vivo). >10 hours (Escherichia coli, in vivo). Instability index: The instability index (II) is computed to be 57.17 This classifies the protein as unstable. Aliphatic index: 86.61 Grand average of hydropathicity (GRAVY): -0.441

3. Trnsmembrane regions of the proteins by ExPASy TMPred (Source: https://embnet.vital-it.ch/cgi-bin/TMPRED_form_parser)

TMpred prediction output for : TMPRED.28636.5237.seq Sequence: MAR...GHT length: 333 Prediction parameters: TM-helix length between 17 and 33 1.) Possible transmembrane helices ================================== The sequence positions in brackets denominate the core region. Only scores above 500 are considered significant. Inside to outside helices : 2 found from to score center 208 ( 208) 226 ( 226) 92 216 258 ( 258) 276 ( 276) 2283 268 Outside to inside helices : 3 found from to score center 77 ( 77) 95 ( 93) 449 85 208 ( 208) 226 ( 224) 266 216 258 ( 260) 276 ( 276) 2916 268 2.) Table of correspondences ============================ Here is shown, which of the inside->outside helices correspond to which of the outside->inside helices. Helices shown in brackets are considered insignificant. A "+" symbol indicates a preference of this orientation. A "++" symbol indicates a strong preference of this orientation. inside->outside | outside->inside |( 77- 95 (19) 449 ++ ) ( 208- 226 (19) 92 ) |( 208- 226 (19) 266 + ) 258- 276 (19) 2283 | 258- 276 (19) 2916 ++ 3.) Suggested models for transmembrane topology =============================================== These suggestions are purely speculative and should be used with EXTREME CAUTION since they are based on the assumption that all transmembrane helices have been found. In most cases, the Correspondence Table shown above or the prediction plot that is also created should be used for the topology assignment of unknown proteins. 2 possible models considered, only significant TM-segments used -----> STRONGLY prefered model: N-terminus outside 1 strong transmembrane helices, total score : 2916 # from to length score orientation 1 258 276 (19) 2916 o-i ------> alternative model 1 strong transmembrane helices, total score : 2283 # from to length score orientation 1 258 276 (19) 2283 i-o

You can get the prediction graphics shown above in one of the following formats:

• GIF-format

4. The subcellular organization protein: ExPASy DAS-TMfilter (source: http://mendel.imp.ac.at/sat/DAS/cgi-bin/das.cgi)

Calculating prediction for the following proteins with reference library 08: > ... Done. *** List of predicted non-TM-protein codes *** none *** List of predicted TM-protein codes *** > === Result of the prediction === > # TMH: 1 Q: 0.93 @ 266 5.185 core: 259 .. 274 5.406e-06 <-------- end of list -------->