Week 4 HW: Protein Design Part I

Part A: Conceptual Questions

We were allowed answer 9 out of 11 of the following questions:

How many molecules of amino acids do you take with a piece of 500 grams of meat? (on average an amino acid is ~100 Daltons)

I expect answers to vary since meat composition vary.

Water composition of meat is estimated to be about 65-80% meat. Some estimates have proteins make up around 1/5 to less than 1/3 of overall muscle tissue.

We’ll work with 20% and 30% for upper and lower bounds for simplicity.

Assuming that 100 Daltons roughly equals 100 g/mo

Lower: 500 g × 0.2 = 100 g protein = 1 mol. 6.02 × 10²³ molecules

Upper: 500 g × 0.3 = 150 g protein = 1.5 mol. ~9 × 10²³ molecules

Quick Sources: https://redtablemeats.com/fresh-meat/beef/what-percentage-of-beef-is-protein/ https://agriculture.institute/fresh-meat-technology/water-content-in-meat-importance/

For simplicity, let’s work with Taking the average, 500 grams of meat may yield

Why do humans eat beef but do not become a cow, eat fish but do not become fish?

These products are broken down through digestion and recycled. Our genetic material largely informs the building process of new material.

Why are there only 20 natural amino acids?

I’m not convinced that those are the only ones, in so far of what we have observed on Earth it is likely that the developmental “cost” as per our development over time was too high. 20 reflects optimization, no?

Can you make other non-natural amino acids? Design some new amino acids.

Yes. These can be designed through new side chains, although stability and inclusion may be a problem.

Where did amino acids come from before enzymes that make them, and before life started?

Abiotic processes. Some sources list thermal vents and delivery through meteorites.

Ehrenfreund, P., Bernstein, M.P., Dworkin, J.P., Sandford, S.A. and Allamandola, L.J., 2001. The photostability of amino acids in space. The Astrophysical Journal Letters, 550(1), pp.L95-L99.

Kobayashi, K., Mita, H., Kebukawa, Y., Nakagawa, K., Kaneko, T., Obayashi, Y., Sato, T., Yokoo, T., Minematsu, S., Fukuda, H. and Oguri, Y., 2021. Space exposure of amino acids and their precursors during the Tanpopo Mission. Astrobiology, 21(12), pp.1479-1493.

If you make an α-helix using D-amino acids, what handedness (right or left) would you expect?

Left-handed

Can you discover additional helices in proteins?

Yes

Why are most molecular helices right-handed?

The stereochemistry of L-amino acids constrains backbone geometry in a way that right-handed helices are lower in energy. Right-handed chirality is favored and chirality from the bottom influences chirality at higher structures.

Why do β-sheets tend to aggregate? What is the driving force for β-sheet aggregation?

[Skipped]

Why do many amyloid diseases form β-sheets?

β-Sheet structures are stable and can easy to produce from misfolding.

Can you use amyloid β-sheets as materials? Design a β-sheet motif that forms a well-ordered structure.

[Skipped]

Part B: Protein Analysis and Visualization

The protein that I selected is U-box domain-containing protein 12.Possesses E3 ubiquitin-protein ligase in vitro. I was not too particular on its selection and wanted to start somewhere.

Source: https://www.uniprot.org/uniprotkb/Q5VRH9/entry

Oryza sativa subsp. japonica (Rice)

Amino Acid sequence:

sp|Q5VRH9|PUB12_ORYSJ U-box domain-containing protein 12 OS=Oryza sativa subsp. japonica OX=39947 GN=PUB12 PE=1 SV=1 MPKRVADEIAALPEPRGPLRRPCADLSRRVRLLAPLLDHLPASSSSSSSTPLADALGAAR DLLRKTRDGSKIDQAMRGDAFLDEFAGVNRQIHLALDALPYNTFHMPQEVQEQVALVHSQ FQRASTRTDPPDTQLSMDLAWALTDNPSDPALLTRISHKLQLHTMADMKNESIALHNMVI STAGEPDGCVDQMSSLLKKLKDCVVTEDHANDALTTRSASIKHRSPIIPDEFRCPISLEL MQDPVIVSSGQTYERSCIQKWLDSGHKTCPKTQQPLSHTSLTPNFVLKSLISQWCEANGI ELPKNKQNSRDKKAAKSSDYDHAGLVSLMNRLRSGNQDEQRAAAGEIRLLAKRNVNNRIC IAEAGAIPLLVNLLSSSDPRTQEHAVTALLNLSIHENNKASIVDSHAIPKIVEVLKTGSM ETRENAAATLFSLSVVDENKVTIGAAGAIPPLINLLCDGSPRGKKDAATAIFNLCIYQGN KVRAVKAGIVIHLMNFLVDPTGGMIDEALSLLSILAGNPEGKIVIARSEPIPPLVEVIKT GSPRNRENAAAILWLLCSADTEQTLAAKAAGVEDALKELSETGTDRAKRKASSILELMHQ ANEDSLKGNGH

The length of the protein is: 611 aminoacids. The most common amino acid is: L, which appears 72 times.

This protein does not share 100% homology with any other although there are many with 50-90% homology, per UniProt. Via the Blast Tool, a lot of homologs were found.

Query= EMBOSS_001

Length=611 Score E Sequences producing significant alignments: (Bits) Value

SP:Q5VRH9 PUB12_ORYSJ U-box domain-containing protein 12 OS=Oryza … 1199 0.0 TR:I1PYP8 I1PYP8_ORYGL U-box domain-containing protein 12 OS=Oryza… 1194 0.0 TR:A0A0D3GBR7 A0A0D3GBR7_9ORYZ RING-type E3 ubiquitin transferase … 1193 0.0 TR:A0A0E0PSC1 A0A0E0PSC1_ORYRU U-box domain-containing protein 12 … 1193 0.0 TR:A0A0E0HJJ2 A0A0E0HJJ2_ORYNI U-box domain-containing protein 12 … 1192 0.0 TR:A0A0E0A3S8 A0A0E0A3S8_9ORYZ U-box domain-containing protein 12 … 1182 0.0 SP:Q5VRH9-2 PUB12_ORYSJ Isoform 2 of U-box domain-containing prote… 1182 0.0 TR:A0A0D3GBR8 A0A0D3GBR8_9ORYZ RING-type E3 ubiquitin transferase … 1176 0.0 TR:A0A0E0PSC3 A0A0E0PSC3_ORYRU U-box domain-containing protein 12 … 1176 0.0 TR:A0A0E0HJJ3 A0A0E0HJJ3_ORYNI U-box domain-containing protein 12 … 1175 0.0 TR:A2Y893 A2Y893_ORYSI U-box domain-containing protein 12 OS=Oryza… 1167 0.0 TR:A0A0E0A3T5 A0A0E0A3T5_9ORYZ U-box domain-containing protein 12 … 1165 0.0 TR:A0A0E0DVD9 A0A0E0DVD9_9ORYZ U-box domain-containing protein 12 … 1165 0.0 TR:A0A0E0L6Q0 A0A0E0L6Q0_ORYPU U-box domain-containing protein 12 … 1152 0.0 TR:A0A6G1DGM2 A0A6G1DGM2_9ORYZ RING-type E3 ubiquitin transferase … 1128 0.0 TR:A0A0D9WKQ8 A0A0D9WKQ8_9ORYZ RING-type E3 ubiquitin transferase … 1102 0.0 TR:A0A0E0A3T4 A0A0E0A3T4_9ORYZ RING-type E3 ubiquitin transferase … 1009 0.0 TR:A0A5J9SK41 A0A5J9SK41_9POAL RING-type E3 ubiquitin transferase … 1005 0.0 TR:A0A2T7E463 A0A2T7E463_9POAL RING-type E3 ubiquitin transferase … 1000 0.0 TR:A0ABC9E206 A0ABC9E206_9POAL RING-type E3 ubiquitin transferase … 999 0.0 TR:A0A3L6RWE2 A0A3L6RWE2_PANMI RING-type E3 ubiquitin transferase … 999 0.0 TR:A0ABC9DBY8 A0ABC9DBY8_9POAL RING-type E3 ubiquitin transferase … 993 0.0 TR:A0A8T0T5H3 A0A8T0T5H3_PANVG RING-type E3 ubiquitin transferase … 993 0.0 TR:A0ABC9DW43 A0ABC9DW43_9POAL RING-type E3 ubiquitin transferase … 991 0.0 TR:A0A1E5WM86 A0A1E5WM86_9POAL RING-type E3 ubiquitin transferase … 991 0.0 TR:A0A811SD54 A0A811SD54_9POAL RING-type E3 ubiquitin transferase … 989 0.0 TR:A0A8T0TI26 A0A8T0TI26_PANVG RING-type E3 ubiquitin transferase … 988 0.0 TR:A0A811S773 A0A811S773_9POAL RING-type E3 ubiquitin transferase … 987 0.0 TR:A0A835KU84 A0A835KU84_9POAL RING-type E3 ubiquitin transferase … 986 0.0 TR:A0AAV5CS17 A0AAV5CS17_ELECO U-box domain-containing protein 12 … 986 0.0 TR:J3MAH2 J3MAH2_ORYBR U-box domain-containing protein 12 OS=Oryza… 985 0.0 TR:C5Z221 C5Z221_SORBI RING-type E3 ubiquitin transferase OS=Sorgh… 984 0.0 TR:A0A835FWE8 A0A835FWE8_9POAL RING-type E3 ubiquitin transferase … 983 0.0 TR:I1H245 I1H245_BRADI U-box domain-containing protein 12 OS=Brach… 983 0.0 TR:A0A3L6PH60 A0A3L6PH60_PANMI RING-type E3 ubiquitin transferase … 982 0.0 TR:A0A4U6UXZ9 A0A4U6UXZ9_SETVI U-box domain-containing protein 12 … 981 0.0 TR:B6SXY9 B6SXY9_MAIZE RING-type E3 ubiquitin transferase OS=Zea m… 964 0.0 TR:A0ACD5Y0V4 A0ACD5Y0V4_AVESA Uncharacterized protein OS=Avena sa… 957 0.0 TR:A0A3B6THH5 A0A3B6THH5_WHEAT RING-type E3 ubiquitin transferase … 956 0.0 TR:A0A8R7RDC8 A0A8R7RDC8_TRIUA RING-type E3 ubiquitin transferase … 955 0.0 TR:A0ACD6A429 A0ACD6A429_AVESA Uncharacterized protein OS=Avena sa… 950 0.0 TR:A0A8I6Y9M9 A0A8I6Y9M9_HORVV RING-type E3 ubiquitin transferase … 942 0.0 TR:A0A3B6I3Q2 A0A3B6I3Q2_WHEAT U-box domain-containing protein 12 … 917 0.0 TR:A0AAV5F2R6 A0AAV5F2R6_ELECO U-box domain-containing protein 12 … 914 0.0 TR:K3XW51 K3XW51_SETIT U-box domain-containing protein 12 OS=Setar… 905 0.0 TR:A0A0E0L6Q1 A0A0E0L6Q1_ORYPU U-box domain-containing protein 12 … 900 0.0 TR:A0A452XGN3 A0A452XGN3_AEGTS RING-type E3 ubiquitin transferase … 888 0.0 TR:A0A3B6R6B6 A0A3B6R6B6_WHEAT RING-type E3 ubiquitin transferase … 868 0.0 TR:A0A9R0Z145 A0A9R0Z145_TRITD RING-type E3 ubiquitin transferase … 866 0.0 TR:A0ACD5ZS62 A0ACD5ZS62_AVESA Uncharacterized protein OS=Avena sa… 843 0.0 TR:A0A452XGJ2 A0A452XGJ2_AEGTS RING-type E3 ubiquitin transferase … 836 0.0 TR:A0A0E0DVD6 A0A0E0DVD6_9ORYZ RING-type E3 ubiquitin transferase … 815 0.0 TR:A0A6I9S1S1 A0A6I9S1S1_ELAGV RING-type E3 ubiquitin transferase … 795 0.0 TR:A0A8B7C1E5 A0A8B7C1E5_PHODC RING-type E3 ubiquitin transferase … 786 0.0 TR:A0AAV8GY30 A0AAV8GY30_9POAL RING-type E3 ubiquitin transferase … 785 0.0 TR:A0AAV8EMN4 A0AAV8EMN4_9POAL RING-type E3 ubiquitin transferase … 783 0.0 TR:A0A8K0IKK4 A0A8K0IKK4_COCNU RING-type E3 ubiquitin transferase … 782 0.0 TR:A0AAV8F803 A0AAV8F803_9POAL RING-type E3 ubiquitin transferase … 781 0.0 TR:A0A8K0N659 A0A8K0N659_COCNU RING-type E3 ubiquitin transferase … 780 0.0 TR:A0A6I9SJB7 A0A6I9SJB7_ELAGV RING-type E3 ubiquitin transferase … 779 0.0 TR:A0A8B8Z9X0 A0A8B8Z9X0_PHODC U-box domain-containing protein 12 … 778 0.0 TR:A0A9Q0CB42 A0A9Q0CB42_9POAL RING-type E3 ubiquitin transferase … 777 0.0 TR:A0AAD5WDJ8 A0AAD5WDJ8_9POAL RING-type E3 ubiquitin transferase … 776 0.0 TR:A0A452XGQ0 A0A452XGQ0_AEGTS RING-type E3 ubiquitin transferase … 773 0.0 TR:A0A2I0BCA5 A0A2I0BCA5_9ASPA RING-type E3 ubiquitin transferase … 757 0.0 TR:A0A3B6TG51 A0A3B6TG51_WHEAT RING-type E3 ubiquitin transferase … 756 0.0 TR:A0A835RLE0 A0A835RLE0_VANPL RING-type E3 ubiquitin transferase … 755 0.0 TR:A0A9R0SRI3 A0A9R0SRI3_TRITD U-box domain-containing protein 12 … 754 0.0 TR:A0A6I9S1Y4 A0A6I9S1Y4_ELAGV RING-type E3 ubiquitin transferase … 753 0.0 TR:A0A833VES7 A0A833VES7_9POAL RING-type E3 ubiquitin transferase … 751 0.0 TR:A0A9R1BGT5 A0A9R1BGT5_TRITD RING-type E3 ubiquitin transferase … 751 0.0 TR:A0A9D5BZQ6 A0A9D5BZQ6_9LILI RING-type E3 ubiquitin transferase … 750 0.0 TR:A0ABD0UM27 A0ABD0UM27_DENTH RING-type E3 ubiquitin transferase … 746 0.0 TR:A0A8B8ZB12 A0A8B8ZB12_PHODC RING-type E3 ubiquitin transferase … 745 0.0 TR:A0A8T3AWN2 A0A8T3AWN2_DENNO RING-type E3 ubiquitin transferase … 744 0.0 TR:A0A2I0WEQ6 A0A2I0WEQ6_9ASPA RING-type E3 ubiquitin transferase … 743 0.0 TR:A0A6P5GVN1 A0A6P5GVN1_ANACO RING-type E3 ubiquitin transferase … 741 0.0 TR:A0A5P1FQ11 A0A5P1FQ11_ASPOF RING-type E3 ubiquitin transferase … 734 0.0 TR:A0AAP0G926 A0AAP0G926_9ASPA RING-type E3 ubiquitin transferase … 729 0.0 TR:A0AAP0WZL6 A0AAP0WZL6_LIQFO RING-type E3 ubiquitin transferase … 728 0.0 TR:A0A843WFY6 A0A843WFY6_COLES RING-type E3 ubiquitin transferase … 723 0.0 TR:A0ACB7WUI3 A0ACB7WUI3_DIOAL Zinc finger RING/FYVE/PHD-type prot… 723 0.0 TR:A0AB40BCZ8 A0AB40BCZ8_DIOCR RING-type E3 ubiquitin transferase … 723 0.0 TR:A0AAQ3K0H0 A0AAQ3K0H0_9LILI RING-type E3 ubiquitin transferase … 720 0.0 TR:F6HND8 F6HND8_VITVI RING-type E3 ubiquitin transferase OS=Vitis… 718 0.0 TR:A0ABY9D2S6 A0ABY9D2S6_VITVI RING-type E3 ubiquitin transferase … 718 0.0 TR:A0AAV7E209 A0AAV7E209_ARIFI RING-type E3 ubiquitin transferase … 717 0.0 TR:A0AA39DJS7 A0AA39DJS7_VITRO RING-type E3 ubiquitin transferase … 715 0.0 TR:A0ABS8SCS2 A0ABS8SCS2_DATST RING-type E3 ubiquitin transferase … 712 0.0 TR:A0AAV5LAD4 A0AAV5LAD4_9ROSI RING-type E3 ubiquitin transferase … 712 0.0 TR:V4TIZ6 V4TIZ6_CITCL RING-type E3 ubiquitin transferase OS=Citru… 710 0.0 TR:A0A804I6U7 A0A804I6U7_MUSAM RING-type E3 ubiquitin transferase … 710 0.0 TR:A0A200Q9A7 A0A200Q9A7_MACCD RING-type E3 ubiquitin transferase … 709 0.0 TR:A0A7J6W5Z9 A0A7J6W5Z9_THATH RING-type E3 ubiquitin transferase … 709 0.0 TR:A0ACB8L513 A0ACB8L513_CITSI U-box domain-containing protein 14 … 709 0.0 TR:A0A067E149 A0A067E149_CITSI RING-type E3 ubiquitin transferase … 709 0.0 TR:A0ACB9PUD9 A0ACB9PUD9_BAUVA Uncharacterized protein OS=Bauhinia… 707 0.0 TR:A0A9Q1MDB3 A0A9Q1MDB3_9SOLA RING-type E3 ubiquitin transferase … 707 0.0 TR:A0AAV8RJ11 A0AAV8RJ11_ENSVE RING-type E3 ubiquitin transferase … 707 0.0 TR:A0AAN8VNY8 A0AAN8VNY8_9MAGN RING-type E3 ubiquitin transferase … 706 0.0 TR:A0ABR2QF73 A0ABR2QF73_9ROSI RING-type E3 ubiquitin transferase … 706 0.0 TR:A0A061FPF5 A0A061FPF5_THECC RING-type E3 ubiquitin transferase … 706 0.0 TR:A0A6P5YZR2 A0A6P5YZR2_DURZI RING-type E3 ubiquitin transferase … 705 0.0 TR:A0A6A4QEE0 A0A6A4QEE0_LUPAL RING-type E3 ubiquitin transferase … 705 0.0 TR:A0A6I9TG78 A0A6I9TG78_SESIN RING-type E3 ubiquitin transferase … 705 0.0 TR:A0A835LLS2 A0A835LLS2_9MAGN RING-type E3 ubiquitin transferase … 705 0.0 TR:A0AAD4NZN1 A0AAD4NZN1_PERFH RING-type E3 ubiquitin transferase … 704 0.0 TR:A0ABR2S2R6 A0ABR2S2R6_9ROSI RING-type E3 ubiquitin transferase … 704 0.0 TR:A0AAE1RYG1 A0AAE1RYG1_9SOLA RING-type E3 ubiquitin transferase … 704 0.0 TR:A0A1J6IL89 A0A1J6IL89_NICAT RING-type E3 ubiquitin transferase … 704 0.0 TR:A0A9Q1M5W7 A0A9Q1M5W7_9SOLA RING-type E3 ubiquitin transferase … 704 0.0 TR:A0A6J1B7W8 A0A6J1B7W8_9ROSI RING-type E3 ubiquitin transferase … 704 0.0 TR:A0A9W7HPH7 A0A9W7HPH7_HIBTR RING-type E3 ubiquitin transferase … 703 0.0 TR:A0A9W7HNE6 A0A9W7HNE6_HIBTR RING-type E3 ubiquitin transferase … 703 0.0 TR:A0A2P5ANF8 A0A2P5ANF8_TREOI RING-type E3 ubiquitin transferase … 702 0.0 TR:A0A1S2XZS7 A0A1S2XZS7_CICAR RING-type E3 ubiquitin transferase … 702 0.0 TR:A0AAE1SAH3 A0AAE1SAH3_9SOLA RING-type E3 ubiquitin transferase … 702 0.0 TR:A0A1J7FNJ6 A0A1J7FNJ6_LUPAN RING-type E3 ubiquitin transferase … 702 0.0 TR:A0A2P5AJ14 A0A2P5AJ14_PARAD RING-type E3 ubiquitin transferase … 702 0.0 TR:A0A1U7VEA5 A0A1U7VEA5_NICSY RING-type E3 ubiquitin transferase … 702 0.0 TR:M1ABT1 M1ABT1_SOLTU RING-type E3 ubiquitin transferase OS=Solan… 702 0.0 TR:A0ABQ7W6L0 A0ABQ7W6L0_SOLTU RING-type E3 ubiquitin transferase … 702 0.0 TR:A0AAV9K3G9 A0AAV9K3G9_9SOLN RING-type E3 ubiquitin transferase … 702 0.0 TR:A0A1S4BCS6 A0A1S4BCS6_TOBAC RING-type E3 ubiquitin transferase … 702 0.0 TR:A0A6J5U2T1 A0A6J5U2T1_PRUAR RING-type E3 ubiquitin transferase … 702 0.0 TR:A0ACB8L4W7 A0ACB8L4W7_CITSI U-box domain-containing protein 14 … 702 0.0 TR:A0A2G2VCI1 A0A2G2VCI1_CAPBA RING-type E3 ubiquitin transferase … 702 0.0 TR:A0AAE1YU04 A0AAE1YU04_9LAMI RING-type E3 ubiquitin transferase … 701 0.0 TR:A0AAV1X6J7 A0AAV1X6J7_LUPLU RING-type E3 ubiquitin transferase … 701 0.0 TR:A0A1U8EX65 A0A1U8EX65_CAPAN RING-type E3 ubiquitin transferase … 701 0.0 TR:A0A5E4ECC4 A0A5E4ECC4_PRUDU RING-type E3 ubiquitin transferase … 701 0.0 TR:A0ABD1WYG0 A0ABD1WYG0_9LAMI RING-type E3 ubiquitin transferase … 701 0.0 TR:A0AAD7M5U3 A0AAD7M5U3_QUISA RING-type E3 ubiquitin transferase … 701 0.0 TR:A0AAD7Q5P3 A0AAD7Q5P3_QUISA RING-type E3 ubiquitin transferase … 700 0.0 TR:A0A6P8CYA9 A0A6P8CYA9_PUNGR RING-type E3 ubiquitin transferase … 700 0.0 TR:A0A1S3ZKQ3 A0A1S3ZKQ3_TOBAC RING-type E3 ubiquitin transferase … 700 0.0 TR:A0A2G5D164 A0A2G5D164_AQUCA RING-type E3 ubiquitin transferase … 700 0.0 TR:A0A6P5U3J9 A0A6P5U3J9_PRUAV RING-type E3 ubiquitin transferase … 700 0.0 TR:A0ABQ9M5E9 A0ABQ9M5E9_HEVBR RING-type E3 ubiquitin transferase … 699 0.0 TR:A0ACC0ZAK8 A0ACC0ZAK8_9ROSI Uncharacterized protein OS=Pistacia… 699 0.0 TR:A0ABM0P219 A0ABM0P219_PRUMU RING-type E3 ubiquitin transferase … 699 0.0 TR:A0A3Q7IQ73 A0A3Q7IQ73_SOLLC RING-type E3 ubiquitin transferase … 699 0.0 TR:A0AA39SE18 A0AA39SE18_ACESA RING-type E3 ubiquitin transferase … 699 0.0 TR:A0A5J5AW04 A0A5J5AW04_9ASTE RING-type E3 ubiquitin transferase … 699 0.0 TR:A0A314Y6E1 A0A314Y6E1_PRUYE RING-type E3 ubiquitin transferase … 699 0.0 TR:A0A251QMB1 A0A251QMB1_PRUPE RING-type E3 ubiquitin transferase … 699 0.0 TR:A0A7J7M6E3 A0A7J7M6E3_9MAGN RING-type E3 ubiquitin transferase … 699 0.0 TR:A0AAV1QYQ7 A0AAV1QYQ7_9ROSI RING-type E3 ubiquitin transferase … 699 0.0 TR:A0A835H9Y2 A0A835H9Y2_9MAGN RING-type E3 ubiquitin transferase … 699 0.0 TR:A0AAD4XDG0 A0AAD4XDG0_9MAGN RING-type E3 ubiquitin transferase … 698 0.0 TR:A0AAE1ILH4 A0AAE1ILH4_9FABA RING-type E3 ubiquitin transferase … 698 0.0 TR:A0A8J6CUL5 A0A8J6CUL5_9ROSI RING-type E3 ubiquitin transferase … 698 0.0 TR:A0ABD2QVW4 A0ABD2QVW4_9SOLN RING-type E3 ubiquitin transferase … 697 0.0 TR:A0A5N5FI06 A0A5N5FI06_9ROSA RING-type E3 ubiquitin transferase … 697 0.0 TR:A0A9Q0UCA7 A0A9Q0UCA7_SALPP RING-type E3 ubiquitin transferase … 697 0.0 TR:A0AAE0BAR6 A0AAE0BAR6_9ROSI RING-type E3 ubiquitin transferase … 697 0.0 TR:A0ABM1FMC2 A0ABM1FMC2_SOLPN RING-type E3 ubiquitin transferase … 697 0.0 TR:A0A6P6AKQ0 A0A6P6AKQ0_DURZI RING-type E3 ubiquitin transferase … 697 0.0 TR:A0AAP0LDP2 A0AAP0LDP2_9MAGN RING-type E3 ubiquitin transferase … 697 0.0 TR:A0AAP0QEX9 A0AAP0QEX9_9ROSI RING-type E3 ubiquitin transferase … 697 0.0 TR:A0A9J5WGK4 A0A9J5WGK4_SOLCO RING-type E3 ubiquitin transferase … 697 0.0 TR:A0ACB8L597 A0ACB8L597_CITSI U-box domain-containing protein 14 … 697 0.0 TR:A0A5C7GYA8 A0A5C7GYA8_9ROSI RING-type E3 ubiquitin transferase … 697 0.0 TR:A0A5D2XPV8 A0A5D2XPV8_GOSMU RING-type E3 ubiquitin transferase … 697 0.0 TR:A0A8T2Y9A9 A0A8T2Y9A9_POPDE RING-type E3 ubiquitin transferase … 697 0.0 TR:A0ABM2YU16 A0ABM2YU16_GOSHI RING-type E3 ubiquitin transferase … 697 0.0 TR:A0AAN8SZP9 A0AAN8SZP9_SOLBU RING-type E3 ubiquitin transferase … 697 0.0 TR:A0AAD5IAS4 A0AAD5IAS4_ACENE RING-type E3 ubiquitin transferase … 697 0.0 TR:A0A9Q0WKY8 A0A9Q0WKY8_9ROSI RING-type E3 ubiquitin transferase … 696 0.0 TR:A0A5D2NX47 A0A5D2NX47_GOSTO RING-type E3 ubiquitin transferase … 696 0.0 TR:A0ABD3TPL4 A0ABD3TPL4_9LAMI RING-type E3 ubiquitin transferase … 696 0.0 TR:A0A3S4PK96 A0A3S4PK96_9MAGN RING-type E3 ubiquitin transferase … 696 0.0 TR:A0AAD6PFY3 A0AAD6PFY3_9ROSI RING-type E3 ubiquitin transferase … 696 0.0 TR:A0A5J5B9Y0 A0A5J5B9Y0_9ASTE RING-type E3 ubiquitin transferase … 696 0.0 TR:A0ABC8UN55 A0ABC8UN55_9AQUA RING-type E3 ubiquitin transferase … 696 0.0 TR:B9HLH5 B9HLH5_POPTR RING-type E3 ubiquitin transferase OS=Popul… 696 0.0 TR:A0A5D2JAA3 A0A5D2JAA3_GOSTO RING-type E3 ubiquitin transferase … 696 0.0 TR:A0A8K0GRB9 A0A8K0GRB9_9ROSA RING-type E3 ubiquitin transferase … 695 0.0 TR:A0A5D2TDZ1 A0A5D2TDZ1_GOSMU RING-type E3 ubiquitin transferase … 695 0.0 TR:A0A5D2B520 A0A5D2B520_GOSDA RING-type E3 ubiquitin transferase … 695 0.0 TR:A0AAE1X2D8 A0AAE1X2D8_9LAMI RING-type E3 ubiquitin transferase … 695 0.0 TR:A0ABR2BSQ0 A0ABR2BSQ0_9ROSI RING-type E3 ubiquitin transferase … 695 0.0 TR:A0ABR2NSZ0 A0ABR2NSZ0_9ROSI RING-type E3 ubiquitin transferase … 695 0.0 TR:A0ABM3AXC1 A0ABM3AXC1_GOSHI RING-type E3 ubiquitin transferase … 695 0.0 TR:A0AAF0UY34 A0AAF0UY34_SOLVR RING-type E3 ubiquitin transferase … 695 0.0 TR:A0ABC8QLK3 A0ABC8QLK3_9AQUA RING-type E3 ubiquitin transferase … 695 0.0 TR:A0ABC8SRL1 A0ABC8SRL1_9AQUA RING-type E3 ubiquitin transferase … 695 0.0 TR:A0A9Q0SV54 A0A9Q0SV54_SALVM RING-type E3 ubiquitin transferase … 694 0.0 TR:A0ABU6RFH6 A0ABU6RFH6_9FABA RING-type E3 ubiquitin transferase … 694 0.0 TR:A0A8X7Z8K1 A0A8X7Z8K1_POPTO RING-type E3 ubiquitin transferase … 694 0.0 TR:A0ACC4BRY9 A0ACC4BRY9_POPAL Uncharacterized protein OS=Populus … 694 0.0 TR:A0AAD6MJN4 A0AAD6MJN4_9ROSI RING-type E3 ubiquitin transferase … 694 0.0 TR:A0ABD2TIP0 A0ABD2TIP0_9SOLN RING-type E3 ubiquitin transferase … 694 0.0 TR:A0ACC2KS43 A0ACC2KS43_PERAE Uncharacterized protein OS=Persea a… 694 0.0 TR:A0ABD3E7B2 A0ABD3E7B2_9LAMI RING-type E3 ubiquitin transferase … 694 0.0 TR:A0AAP0NZD1 A0AAP0NZD1_9MAGN RING-type E3 ubiquitin transferase … 694 0.0 TR:A0A834W7W7 A0A834W7W7_9FABA RING-type E3 ubiquitin transferase … 694 0.0 TR:A0A5J5PUV7 A0A5J5PUV7_GOSBA RING-type E3 ubiquitin transferase … 694 0.0 TR:A0A0B0NXG6 A0A0B0NXG6_GOSAR RING-type E3 ubiquitin transferase … 694 0.0 TR:A0ABR0NKE6 A0ABR0NKE6_GOSAR Uncharacterized protein OS=Gossypiu… 694 0.0 TR:A0A9D3UIB5 A0A9D3UIB5_9ROSI RING-type E3 ubiquitin transferase … 694 0.0 TR:A0A1R3H5H3 A0A1R3H5H3_COCAP RING-type E3 ubiquitin transferase … 694 0.0 TR:A0ACC2KS90 A0ACC2KS90_PERAE Uncharacterized protein OS=Persea a… 694 0.0 TR:A0AAJ6UKJ1 A0AAJ6UKJ1_POPEU RING-type E3 ubiquitin transferase … 694 0.0 TR:A0ABD1GH90 A0ABD1GH90_SALDI RING-type E3 ubiquitin transferase … 694 0.0 TR:A0A1R3JE18 A0A1R3JE18_9ROSI RING-type E3 ubiquitin transferase … 694 0.0 TR:A0AA88D9K5 A0AA88D9K5_FICCA RING-type E3 ubiquitin transferase … 694 0.0 TR:A0A7J9IC62 A0A7J9IC62_9ROSI RING-type E3 ubiquitin transferase … 693 0.0 TR:A0A7N2R9R8 A0A7N2R9R8_QUELO RING-type E3 ubiquitin transferase … 693 0.0 TR:A0A835JZV4 A0A835JZV4_9ROSI RING-type E3 ubiquitin transferase … 693 0.0 TR:A0A8J5FTW6 A0A8J5FTW6_ZINOF RING-type E3 ubiquitin transferase … 693 0.0 TR:A0A4Y7KVD5 A0A4Y7KVD5_PAPSO RING-type E3 ubiquitin transferase … 693 0.0 TR:A0A5D2F4H4 A0A5D2F4H4_GOSDA RING-type E3 ubiquitin transferase … 693 0.0 TR:A0A8J4VKI5 A0A8J4VKI5_9ROSI RING-type E3 ubiquitin transferase … 693 0.0 TR:A0AAN9F206 A0AAN9F206_CROPI RING-type E3 ubiquitin transferase … 693 0.0 TR:A0A5J5U6C5 A0A5J5U6C5_GOSBA RING-type E3 ubiquitin transferase … 693 0.0 TR:A0A6A2Y6Q4 A0A6A2Y6Q4_HIBSY RING-type E3 ubiquitin transferase … 693 0.0 TR:A0A5B6WJW5 A0A5B6WJW5_9ROSI RING-type E3 ubiquitin transferase … 692 0.0 TR:A0A498JGF4 A0A498JGF4_MALDO RING-type E3 ubiquitin transferase … 692 0.0 TR:A0A7N2MEE7 A0A7N2MEE7_QUELO RING-type E3 ubiquitin transferase … 692 0.0 TR:A0AAV6Y5W4 A0AAV6Y5W4_9LAMI RING-type E3 ubiquitin transferase … 692 0.0 TR:A0AAP0KTP2 A0AAP0KTP2_9MAGN RING-type E3 ubiquitin transferase … 692 0.0 TR:A0A7J6WEB3 A0A7J6WEB3_THATH RING-type E3 ubiquitin transferase … 692 0.0 TR:A0A2G5CD20 A0A2G5CD20_AQUCA RING-type E3 ubiquitin transferase … 692 0.0 TR:W9SKF5 W9SKF5_9ROSA RING-type E3 ubiquitin transferase OS=Morus… 692 0.0 TR:A0A072VQ10 A0A072VQ10_MEDTR U-box domain-containing protein 12 … 692 0.0 TR:A0A9W7I114 A0A9W7I114_HIBTR RING-type E3 ubiquitin transferase … 691 0.0 TR:A0A9W7M2C2 A0A9W7M2C2_HIBTR RING-type E3 ubiquitin transferase … 691 0.0 TR:A0A371F3Y5 A0A371F3Y5_MUCPR RING-type E3 ubiquitin transferase … 691 0.0 TR:A0A8J5FNQ2 A0A8J5FNQ2_ZINOF RING-type E3 ubiquitin transferase … 691 0.0 TR:A0A5N5FBR6 A0A5N5FBR6_9ROSA RING-type E3 ubiquitin transferase … 691 0.0 TR:A0ABC8QLK2 A0ABC8QLK2_9AQUA RING-type E3 ubiquitin transferase … 691 0.0 TR:A0ACB8L5G0 A0ACB8L5G0_CITSI U-box domain-containing protein 14 … 691 0.0 TR:A0ABR0CTF8 A0ABR0CTF8_9LAMI RING-type E3 ubiquitin transferase … 691 0.0 TR:A0A1U7ZJ54 A0A1U7ZJ54_NELNU RING-type E3 ubiquitin transferase … 691 0.0 TR:A0A540L773 A0A540L773_MALBA RING-type E3 ubiquitin transferase … 691 0.0 TR:A0ACB9ZMC7 A0ACB9ZMC7_CATRO Uncharacterized protein OS=Catharan… 691 0.0 TR:A0A1U7Z4U1 A0A1U7Z4U1_NELNU RING-type E3 ubiquitin transferase … 691 0.0 TR:A0A8B8MC51 A0A8B8MC51_ABRPR RING-type E3 ubiquitin transferase … 691 0.0 TR:A0A822YGE3 A0A822YGE3_NELNU RING-type E3 ubiquitin transferase … 691 0.0 TR:A0A7J7CI66 A0A7J7CI66_TRIWF RING-type E3 ubiquitin transferase … 690 0.0 TR:A0A8X8ZET3 A0A8X8ZET3_SALSN U-box domain-containing protein 12 … 690 0.0 TR:A0ACB7HJV7 A0ACB7HJV7_MANES Uncharacterized protein OS=Manihot … 690 0.0 TR:A0A2P6SJA1 A0A2P6SJA1_ROSCH RING-type E3 ubiquitin transferase … 690 0.0 TR:A0A2Z7BEP1 A0A2Z7BEP1_9LAMI RING-type E3 ubiquitin transferase … 689 0.0 TR:A0A8X8ZH43 A0A8X8ZH43_SALSN RING-type E3 ubiquitin transferase … 689 0.0 TR:A0A8S0SA15 A0A8S0SA15_OLEEU RING-type E3 ubiquitin transferase … 689 0.0 TR:A0AAW2CXI6 A0AAW2CXI6_9ROSI RING-type E3 ubiquitin transferase … 689 0.0 TR:A0ACC1YBU1 A0ACC1YBU1_MELAZ RING-type E3 ubiquitin transferase … 689 0.0 TR:A0AAV1C6C9 A0AAV1C6C9_OLDCO RING-type E3 ubiquitin transferase … 689 0.0

This belongs to the U-box E3 ubiquitin ligase family.

1. [Structure page for protein via RCSB]

Name: U-box domain-containing protein 12 Organism: Oryza sativa Japonica Group Experimental Method: X-ray Resolution: 2.5 Å Molecular Weight: 8.952 kDa

The resolution is 2.5 Å indicating good quality.
There are no other molecules in the solved structure
The structure contains only the protein and no additional bound molecules.
It belongs to the U-box structural family.

I used 3D Protein Imager, located at https://3dproteinimaging.com/. I found it via https://bcrf.biochem.wisc.edu/2024/02/06/3d-protein-imager-a-pymol-qutemol-web-alternative/. https://doi.org/10.1093/bioinformatics/btaa009

This can be accessed online, and free. They also provide an illustration service, which is pretty cool. It can be found below. This program did not have the “cartoon”, “ribbon”, and “ball and stick”, but it did have the “Real”, “Outline”, and “Goodsell” (cartoon-like) view modes where are shown from a “Sphere” mode of viewing. See image below.

To visualize it differently, I looked at it from a “tube” viewing mode. It has more helices than sheets. See image below.

Hydrophobic residues are inside the protein core, and hydrophilic residues are on the surface. See image below. Labeling by residue it has many charged and hydrophobic residues, with the latter being more focused inward. See image below.

Visualizing the surface, this structure appears compact, without deep binding cavities. See image below.

Part C

To be added with images

Part D

This part involved several of us students brainstorming for a lab according to the following instructions:

1. Find a group of ~3–4 students
1. Read through the Phage Reading material.
1. Review the Bacteriophage Final Project Goals for engineering the L Protein:
Choose one or two main goals from the list that you think you can address computationally (e.g., “We’ll try to stabilize the lysis protein,” or “We’ll attempt to disrupt its interaction with E. coli DnaJ.”).
Write a 1-page proposal (bullet points or short paragraphs) describing:
Each individually put your plan on your HTGAA website

Our initial proposal can be found below: