User:Nkuldell:M13 redesign
From OpenWetWare
(Difference between revisions)
Current revision (13:58, 26 October 2006) (view source) |
|||
| (7 intermediate revisions not shown.) | |||
| Line 1: | Line 1: | ||
| + | [[M13 redesign, expt'l details]] | ||
==Due Diligence== | ==Due Diligence== | ||
| - | |||
===M13 phage proteins=== | ===M13 phage proteins=== | ||
| - | NCBI link to seq: [[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=56713234]] <br> | + | [[Image:Macintosh HD-Users-nkuldell-Desktop-M13K07 plasmid-phageproteins.jpeg|thumb|left|500px| phage proteins]] |
| - | Source: Phage Display of Peptides and Proteins: a laboratory manual. Kay, Winter, McCafferty. Ch 1. [[http://www.amazon.com/Phage-Display-Peptides-Proteins-Laboratory/dp/0124023800]]<br> | + | [[Image:Macintosh HD-Users-nkuldell-Desktop-M13K07 plasmid-phageparticle.jpeg|thumb|left| phage particle cartoon]] <br> <br> <br> |
| + | *NCBI link to seq: [[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=56713234]] <br> | ||
| + | *Source: Phage Display of Peptides and Proteins: a laboratory manual. Kay, Winter, McCafferty. Ch 1. [[http://www.amazon.com/Phage-Display-Peptides-Proteins-Laboratory/dp/0124023800]]<br> | ||
{| border="1" | {| border="1" | ||
! protein | ! protein | ||
| Line 13: | Line 15: | ||
| 348 | | 348 | ||
| assembly | | assembly | ||
| - | | | + | | includes gXI within, the two form structure in cytoplasmic membrane for phage maturation |
|- | |- | ||
| II | | II | ||
| 410 | | 410 | ||
| replication of DNA + strand | | replication of DNA + strand | ||
| - | | | + | | includes gX within |
|- | |- | ||
| III | | III | ||
| 406 | | 406 | ||
| phage tail protein (5 copies) | | phage tail protein (5 copies) | ||
| - | | | + | | tag at N-term |
|- | |- | ||
| IV | | IV | ||
| 405 | | 405 | ||
| assembly | | assembly | ||
| - | | | + | | organizes to pore in OM |
|- | |- | ||
| V | | V | ||
| 87 | | 87 | ||
| binds ssDNA | | binds ssDNA | ||
| - | | | + | | recognizes DNA PS |
|- | |- | ||
| VI | | VI | ||
| 112 | | 112 | ||
| phage tail protein (5 copies) | | phage tail protein (5 copies) | ||
| - | | | + | | packages with pIII |
|- | |- | ||
| VII | | VII | ||
| 33 | | 33 | ||
| phage head protein (5 copies) | | phage head protein (5 copies) | ||
| - | | | + | | packages with p9 |
|- | |- | ||
| VIII | | VIII | ||
| 50 | | 50 | ||
| phage coat protein (2700 copies) | | phage coat protein (2700 copies) | ||
| - | | | + | | seg seq cleaved, matured form at aa 23 = clones to N-term, "Petrenko" site [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=8888146&query_hl=2&itool=pubmed_docsum]] |
|- | |- | ||
| IX | | IX | ||
| 32 | | 32 | ||
| phage head protein (5 copies) | | phage head protein (5 copies) | ||
| - | | | + | | stop codon overlaps start of gVIII |
|- | |- | ||
| X | | X | ||
| 111 | | 111 | ||
| DNA replication | | DNA replication | ||
| - | | | + | | internal reinitiation inside gII |
|- | |- | ||
| XI | | XI | ||
| 108 | | 108 | ||
| assembly | | assembly | ||
| - | | | + | | translation reinitiation inside gI |
|} | |} | ||
| - | === | + | |
| - | + | ===Life Cycle of the Phage=== | |
| - | + | [[Image:Macintosh HD-Users-nkuldell-Desktop-M13K07 plasmid-M13lifecycle.jpeg|thumb|left|350px| cartoon depiction for life cycle of M13]] | |
| - | + | [[Image:Macintosh HD-Users-nkuldell-Desktop-M13K07 plasmid-lifecycle key.jpeg|thumb|left|500px| key]] | |
==Makeover ideas== | ==Makeover ideas== | ||
===phage or phage coat rewrite=== | ===phage or phage coat rewrite=== | ||
===separate 8, 9, 3=== | ===separate 8, 9, 3=== | ||
===two copies of 8=== | ===two copies of 8=== | ||
Current revision
Contents |
Due Diligence
M13 phage proteins
- NCBI link to seq: [[1]]
- Source: Phage Display of Peptides and Proteins: a laboratory manual. Kay, Winter, McCafferty. Ch 1. [[2]]
| protein | aa (mature) | function | notes |
|---|---|---|---|
| I | 348 | assembly | includes gXI within, the two form structure in cytoplasmic membrane for phage maturation |
| II | 410 | replication of DNA + strand | includes gX within |
| III | 406 | phage tail protein (5 copies) | tag at N-term |
| IV | 405 | assembly | organizes to pore in OM |
| V | 87 | binds ssDNA | recognizes DNA PS |
| VI | 112 | phage tail protein (5 copies) | packages with pIII |
| VII | 33 | phage head protein (5 copies) | packages with p9 |
| VIII | 50 | phage coat protein (2700 copies) | seg seq cleaved, matured form at aa 23 = clones to N-term, "Petrenko" site [[3]] |
| IX | 32 | phage head protein (5 copies) | stop codon overlaps start of gVIII |
| X | 111 | DNA replication | internal reinitiation inside gII |
| XI | 108 | assembly | translation reinitiation inside gI |
Life Cycle of the Phage
