Molecular Playground/Ubiquitin salt bridge discussion

This page is going to talk about a gas phase or mass spectrum idea about this. From the perspective of solution phase, we can know the salt bridges stay between E51-R54, R54-D58, E18-K29, D21-K29 and K27-D52. And there is one opinion that most protein when electrosprayed into gas phase from its native solution, the structure features will retain mostly. And electron based dissociation method, like ECD or ETD, can break the protein back bonds instead of disrupting its structure.

Once we have one electron based dissociation pattern of ubiquitin, which in real world does not either break any salt bridge above. For reference, ubiquitin's sequence is below:

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

From this particular sequence, there are 11 D and Es as well as 11 R and Ks. Imagine how many possibile salt bridge patterns if all those residues formed randomly. Based on the electron dissociation data, we can eliminate those pattern inside which salt bridges are broken. so, we can get the number of possible or reasonable patterns. Here it is, only 1 percent of the millions of possibilities go into the team of "preserving the salt bridge". This result also supports the statement that protein can stay native when ESIed into gas phase which is so important aspect for analyst who works on mass spectrometry.

This discussion facilitates JAVA by algorithm of premutation and combination. Premutation and combination generate the random pattern which is passed into the mass spectrom result to tell how much salt bridge breaking it happens.All the ideas, coding and running program are acchieved in Nov. 2012 by Zhe Zhang in Richard W. Vachet's lab. For further information or detail, please contact zhez@chem.umass.edu.