[ccp4bb] is codon optimization worth it?

2011-09-30 Thread Patrick Loll
Has anyone encountered a case in which a construct with the native sequence expressed poorly (or not at all?) in Rosetta(DE3), but the corresponding construct with a codon-optimized sequence expressed well? (The gene in question is from cerevesiae) Thanks, Pat

Re: [ccp4bb] is codon optimization worth it?

2011-09-30 Thread Ed Pozharski
On Fri, 2011-09-30 at 10:49 -0400, Patrick Loll wrote: Has anyone encountered a case in which a construct with the native sequence expressed poorly (or not at all?) in Rosetta(DE3), but the corresponding construct with a codon-optimized sequence expressed well? (The gene in question is from

Re: [ccp4bb] is codon optimization worth it?

2011-09-30 Thread Craig A. Bingman
Rosetta strains carry a plasmid that supplies several tRNAs that match codons that are rare in E. coli. This is quite different than being explicitly optimized to express mammalian proteins. We (the Center for Eukaryotic Structural Genomics, a PSI-1 and PSI-2 center) used strains with the

Re: [ccp4bb] is codon optimization worth it?

2011-09-30 Thread Tim Keys
of Patrick Loll Sent: Fri 30.09.2011 16:49 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] is codon optimization worth it? Has anyone encountered a case in which a construct with the native sequence expressed poorly (or not at all?) in Rosetta(DE3), but the corresponding construct with a codon

Re: [ccp4bb] is codon optimization worth it?

2011-09-30 Thread Dima Klenchin
In theory, if the rare codons are all covered by Rosetta's extra tRNAs, codon optimization should not make any difference. In practice it does because frequently it's not codon optimization per se but changing local mRNA structure. - Dima

Re: [ccp4bb] is codon optimization worth it?

2011-09-30 Thread Segelke, Brent W.
bulletin board on behalf of Patrick Loll Sent: Fri 30.09.2011 16:49 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] is codon optimization worth it? Has anyone encountered a case in which a construct with the native sequence expressed poorly (or not at all?) in Rosetta(DE3), but the corresponding

Re: [ccp4bb] is codon optimization worth it?

2011-09-30 Thread Segelke, Brent W.
. Brent From: Anastassis Perrakis [mailto:abba...@gmail.com] On Behalf Of Anastassis Perrakis Sent: Friday, September 30, 2011 10:08 AM To: Segelke, Brent W. Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] is codon optimization worth it? Well, codon optimization is not really trouble, it's money

Re: [ccp4bb] is codon optimization worth it?

2011-09-30 Thread Anastassis Perrakis
@JISCMAIL.AC.UK] On Behalf Of Tim Keys Sent: Friday, September 30, 2011 8:29 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] is codon optimization worth it? We codon optimised a poorly expressed gene from neisseria meningitides based on a codon usage table derived from the Welch (etal

Re: [ccp4bb] is codon optimization worth it?

2011-09-30 Thread Torres-Larios Alfredo
 We recently published something really old-related about it: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0021035 My two cents. Best, Alfredo. Alfredo Torres-Larios, PhD Assistant Professor Instituto de Fisiologia Celular, UNAM Mexico

Re: [ccp4bb] is codon optimization worth it?

2011-09-30 Thread Luca Jovine
, Brent W. Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] is codon optimization worth it? Well, codon optimization is not really trouble, it's money. The money are worth it usually anyway, since the optimized genes are easy to clone if you make many constructs out of one gene, as you better