Side chains numeration of proteins (example Cytochrome C)


by Lindsayyyy
Tags: chains, cytochrome, numeration, proteins
Lindsayyyy
Lindsayyyy is offline
#1
Jan7-14, 10:41 AM
P: 208
Hi everybody,

I hope I'm in the right forum. I have a question concerning the side chain numeration. I was reading the following paper

http://www.ncbi.nlm.nih.gov/pubmed/22927377

and they used the some of the following names for the side chains: M65, H33 etc.

What does that mean? What does the M stand for in M65? At first I thought its the one letter code for amino acids, but I'm wrong. Can anyone help me out with this? I'm quite new to the subject. I tried to google it, but I failed.

Thanks for your help
Phys.Org News Partner Chemistry news on Phys.org
First view of nature-inspired catalyst after ripping hydrogen apart provides insights for better, cheaper fuel cells
Following a protein's travel inside cells is key to improving patient monitoring, drug development
Team helps cancer treatment drugs get past their sticking point
Ygggdrasil
Ygggdrasil is offline
#2
Jan7-14, 12:08 PM
Other Sci
Sci Advisor
P: 1,342
You are correct about the letters standing for the one letter amino acid codes (so M65 is the methionine at position 65, H33 is the histidine at position 33). I think what's throwing you off is the numbering. Some people count the initial methionine in the sequence as amino acid #1, but often this methionine gets removed during post-translational processing of the protein. In these cases, scientists will often take amino acid number 1 as the amino acid following the initiator methionine (in the case of the horse cytochrome c used in the paper, this would be G1, glycine-1).

In case it's helpful, you can find the amino acid sequence for horse cyt c here (although the numbering system is off by one from the numbering system used by the paper you reference):

http://www.uniprot.org/uniprot/P00004#section_seq


Register to reply

Related Discussions
Why are acidic amino acid side chains acidic? Chemistry 4
Poset, Chains and anti-chains Calculus & Beyond Homework 0
Cytochrome P450 Biology 5
difference between fibrous proteins and globular proteins Biology, Chemistry & Other Homework 0
slime mold proteins and/or brain proteins? Biology 0