tag:blogger.com,1999:blog-37148773.post8111994024091614890..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: Monday's Molecule #155Larry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger15125tag:blogger.com,1999:blog-37148773.post-59461574897678222492012-01-13T10:30:59.624-05:002012-01-13T10:30:59.624-05:00It's okay, I'm not a graduate student anyw...It's okay, I'm not a graduate student anyway and I'm from Denmark so we'll probably never meet, I just like following your blog. For some reason, learning about science, biochemistry and evolution is more effective when it's explained <b>how</b> people who lie and obfuscate intentionally, are wrong.Rumrakethttp://www.rationalskepticism.org/member/Rumraket/noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-54015990547495375742012-01-11T15:35:18.837-05:002012-01-11T15:35:18.837-05:00Dima said,
... Rumraket got it right almost an ho...Dima said,<br /><br /><i>... Rumraket got it right almost an hour an a half earlier than I did</i><br /><br />You can't win if you use a pseudonym.Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-37035983068520440512012-01-11T14:08:26.505-05:002012-01-11T14:08:26.505-05:00Larry, but Rumraket got it right almost an hour an...Larry, but Rumraket got it right almost an hour an a half earlier than I did. The skipjack tuna has the same partial sequence (PDB ID 1CYC): <br /><br />>1CYC:A|PDBID|CHAIN|SEQUENCE<br />GDVAKGKKTFVQKCAQCHTVENGGKHKVGPNLWGLFGRKTGQAEGYSYTDANKSKGIVWNENTLMEYLENPKKYIPGTKMIFAGIKKKGERQDLVAYLKSATSDima Klenchinnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-28450282779232065502012-01-10T14:37:55.550-05:002012-01-10T14:37:55.550-05:00I'm going with:
Ferrocytochrome c from Katsuw...I'm going with:<br /><br />Ferrocytochrome c from Katsuwonus pelamis (1CYC)<br /><br />Thunnus alalunga is also a 100% match over the 10aa you gave, but 3CYT is complexed with Protoporphyrin IX, not heme and no sulfur atoms are visible (to me at least) in the structure you've shown. No other ferrocytochrome c structure has a 100% match over those particular 10aa.Andrea T-Nnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-23681087896365251362012-01-10T14:34:21.466-05:002012-01-10T14:34:21.466-05:00Larry-
It is cytochrome C from the large yellow c...Larry-<br /><br />It is cytochrome C from the large yellow croaker, Larimichthys crocea.Bill Chaneynoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-82618809267848117602012-01-10T13:37:10.134-05:002012-01-10T13:37:10.134-05:00Larry- The hint made it too easy. I figured out m...Larry- The hint made it too easy. I figured out myself that it was cytochrome after determining that the central molecule was heme, and that the protein was not myoglobin (which at first looked promising). Searching Google with the partial aa sequence gives you the answer on the fourth hit - and your post gets two of the first three hits! -MattMatt Ghttps://www.blogger.com/profile/07745943486966305844noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-21966391242363913102012-01-10T13:28:39.385-05:002012-01-10T13:28:39.385-05:00It is a heme-bound monomeric cytochrome c from Thu...It is a heme-bound monomeric cytochrome c from Thunnus alalunga (Albacore tuna). The gold atom is iron, of course.Matt Ghttps://www.blogger.com/profile/07745943486966305844noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-55430898483609502452012-01-10T09:45:27.857-05:002012-01-10T09:45:27.857-05:00Cytochrome c.
Multiple answers possible on the sp...Cytochrome c.<br /><br />Multiple answers possible on the species portion of the quiz.<br /><br />Google search had an easy time providing an initial lead.<br /><br />Swiss-prot sequence matches:<br /><i>Lampetra tridentata</i><br /><i>Katsuwonus pelamis</i> <br />However, since there is apparently a structure solved, <i>Lampetra</i> is out.<br /><br />Species with sequence matches at RCSB:<br /><br /><i>Thunnus thynnus</i> (northern bluefin tuna)<br />RCSB entries 1LFM, 1I54, 1I55<br /><br /><br /><i>Thunnus alalunga</i> (albacore tuna) <br />RCSB entries 5CYT (supercedes 4CYT), 3CYT (supercedes 1CYT)<br /><br /><i>Katsuwonus pelamis</i> (bonito, skipjack tuna)<br />RCSB entry 1CYCBayesian Bouffant, FCDnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-15901620447790448372012-01-10T09:39:25.399-05:002012-01-10T09:39:25.399-05:00Google told me that it's the small heme protei...Google told me that it's the small heme protein Cytochrome c, this particular one being found in tuna...maybe?Brent Wilsonnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-83028366628211078242012-01-10T08:56:32.804-05:002012-01-10T08:56:32.804-05:00Its obviously a cytochrome c.
Your partial sequenc...Its obviously a cytochrome c.<br />Your partial sequence is conserved in many fishes including the Pacific lamprey, the large yellow croaker, the tuna Thunnus alalunga (albacore)and Bonito (Katsuo). Since crystal structures are available for the latter two, either could be your molecule.Jean-Marc Neuhausnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-2967228828296256672012-01-10T01:23:38.012-05:002012-01-10T01:23:38.012-05:00I knew immediately what it is except, of course, t...I knew immediately what it is except, of course, the species. However, giving a partial sequence is like giving away the whole thing, from A to Z. Two seconds of googling is all it takes. Cytochrome C from tuna (Thunnus thynnus). <br /><br />Can we have the little puzzles back? :-)Dima Klenchinnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-58560608498830962472012-01-10T01:09:17.564-05:002012-01-10T01:09:17.564-05:00cytochrome ccytochrome cI heart proteinsnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-58990751735069716122012-01-10T00:02:14.313-05:002012-01-10T00:02:14.313-05:00Cytochrome C, in species Katsuwonus pelamis (skipj...Cytochrome C, in species <i>Katsuwonus pelamis</i> (skipjack tuna).<br /><br />Not a graduate student, just playing along :)Rumrakethttp://www.rationalskepticism.org/member/Rumraket/noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-87489354530402138712012-01-09T19:13:55.124-05:002012-01-09T19:13:55.124-05:00Cytochrome CCytochrome CAcleronnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-28449861830390170692012-01-09T16:56:47.228-05:002012-01-09T16:56:47.228-05:00Cytochrome c
http://en.wikipedia.org/wiki/Cytochro...Cytochrome c<br />http://en.wikipedia.org/wiki/Cytochrome_cBecki Manthanoreply@blogger.com